There is an easy way to avoid the problem of historical magic.
I said making it our world but magic the whole time is basically impossible. The closest you can get would be having people know there’s magic and it just ended up in a very similar place as our world at this point in time – Sunshine did that, and while there still ended up being a lot of secondary plotholes spawned from it, it worked pretty well overall. But this creates a tissue-paper world, because the moment you start trying to explain how you got to this point, it gets complicated or you realize that there’s just no decent handwave for why we aren’t currently chattel owned either by the fairies or vampires. Plus, if established magic, it’s hard to make your character special.
This story is built around the idea that the modern technological world is opening up contact with the magical one, and Harry is the first openly magic practitioner. That means magic needs to have started mattering recently, because societies generally don’t decide to just ignore the things murdering them.
No one’s sure what exactly determines magic – alignment of the stars, fluctuating levels of aether passing through the planet, a giant dragon that lives in the center of the earth – but for whatever reason, it comes and goes, and it doesn’t even have the decency to taper off gently. At some point, the magic polarity flips and BAM MAGIC.
During the no-magic periods, magical creatures like vampires are completely inactive. I’d go with them just being regular moldering corpses (ooh, plot point – you know how sometimes they fail to move the cemeteries when they flood a place? There’s now a bunch of ancient vampires who came back long after that happened and are now trapped beneath the water rapidly going mad from starvation. You could try to rescue them, or you could leave the damn bloodsuckers – but then you’d better oppose the environmentalists two years later who want to tear down the outdated dam and let the salmon use the river again before their tree-hugging KILLS US ALL!) but apparently whatever the hell the Nevernever is, they hang out there. So, there’s a magic world too, and while no one’s sure if it’s cause or effect, during times of high magic the barrier between the two is almost nonexistent.
This is why people forget about magical creatures – for generations, they actually are just stories. And because they’re just stories, each area’s stories end up changing in different directions, which is why actual vampires are different in such and such a way.
Now, magic survives even in the low-magic periods. There’s still one or two places left fairies can pop in on a full moon every thirteen years, vampires manage to slither in now and again, and wizards can still do some minor magics with a lot of prep work, a group, and maybe a few virgin sacrifices. And from there comes the culture of secrecy, as well as why magic doesn’t seem too advanced – each transition from high to low magic involves a lot of torches and pitchforks. (It’s also why wizards don’t immediately take over the world when the magic turns back on. They need a while to build their power and numbers up again, and get a handle on how magic works now that it’s at full power.)
But, and here’s the fun thing, wizard power is special, because they’re magic users who are otherwise native to the mundane world. It isn’t determined just by what state the worldwide polarity is set to. The reason Harry is a big deal is he’s a young wizard, one born after the magic had kicked in again. The older wizards have gotten a big boost by magic working again, but Harry and any other newbie wizards will be able to outclass them with minimal training.
Harry is special for living at this point in time – because the new kids will be so much stronger than them, wizards aren’t too motivated to give up their secrets, so there’s almost no other people like him.
Where does technology come into this? For whatever reason, when magic returns, it screws with any technology invented after this point. It’s like each contact updates its grasp of physics. Some wizards theorize that it’s actually replacing the laws of physics around magic users with a sort of stripped-down emulation of how things are “supposed” to work as recorded at initial contact. Things that are updated versions of something that existed will screw up (like modern car radios). Things that didn’t exist, like cellphones, just stop working on the spot. Research into this is limited by the fact wizards rarely have any training in scientific rigor, and the three who did only managed to show the community that trying to combine known and brand new technology to see what happens makes charred corpses.
To make it worse for Harry, the date for magic kicking in and the date for new kids born with boosted magic don’t match up (they don’t know why because they already lost their researchers trying to wire cellphones to radios), which is why he’s stuck using stuff from half a century before he was born. This also explains why wizards would be willing to start taking new apprentices at all – the time period immediately after magic kicks back in is a great time to try to restore their numbers, but eventually you hit the superbabies and incentive switches to hoarding your secrets to try to hold on to your power.
That’s right, Harry murdering his teacher is in fact the horror story everyone lived in fear of! (Or maybe they didn’t even realize this would happen and it was only the murder that made them even realize this was an issue and go into lockdown mode.) And that’s why they seem to behave so irrationally about the whole thing, and why to Harry they just look like a bunch of crazy old guys, because like hell they’re going to say that by the way his magic-fu trumps theirs. It also is the closest I can think of for making stalking Harry with a giant sword make any sense, they really really really want him dead but they’re also scared of him coming after them.
This also lets us have other newbie wizards be dangerous, which I think is really important. The new generation of magic users popping up should upset the status quo, they should be a huge unknown, and an untrained newbie finding a book and trying to teach themselves should be a big deal, because books like this should be about living in interesting times.
Since we’re assuming a lot of stuff is lost in the low-magic period, most layman’s knowledge of magic isn’t true. This lets us just avoid the whole question of what original owners of Chicago believed before we killed them and named the place Chicago. If Harry is feeding fairies milk and honey, it’s not working because they like milk and honey, it’s working because they like food in general and Harry doesn’t know better because his education didn’t cover fairies very well, and in fact real wizards know they’re not “fairies”, that’s just what the Europeans called them. (Bonus: by having Harry not always know the difference between story and reality, we can see it actually play out and lead to adventure rather than him announcing that haha, dumb muggles thought they knew shit that’s cute, maybe I’ll lay down some exposition about the reality or maybe I’ll just repeat that you’re dumb.)
And better yet, Harry not knowing much about magic would give him a legitimate reason to be cagey when the police call him. He’s smart and can work stuff out, but he doesn’t directly recognize most magic. He needs the job and he knows they need him (because a novice wizard is better than no magic consultant at all) so he pretends to be way more experienced than he actually is. This also lets us more easily section off any bullshit like “oh man totally a witch” as actually just being his opinion.
What happens is Harry tries to add a bunch of magic justification onto his guesses because they don’t think anything of his actual detective skills when they’re licensed cops but will take his magic explanations semi-seriously, and we end up with him claiming witches hate better. Harry, who’s studying about detective stuff to supplement his magic knowledge, looks at the situation and pegs it as done by a wife or girlfriend. It’s a spell that requires a ton of magically-charged hatred, it’s hitting a guy in the middle of having sex with a prostitute, and it’s killing both of them. If this involved a gun, spurned lover would be top five easy, and the hatred requirement makes it practically certain. And it does seem intuitively true that witches would be meaner than wizards, I mean, you don’t hear about any wizards luring kids in with gingerbread houses! Plus when he made that joke last time the witches just gave him these nasty looks, so obviously they’re a cranky and hateful bunch.
Harry’s a lot more sympathetic if he’s trying to do his best with his limited knowledge. It’s also the best way to keep him from being too overpowered or too outclassed – as the scale ramps up, Harry learns more to meet the challenges. That’s why every shonen manga ever has the main character have a huge amount of natural talent and no actual experience.
(Incidentally, sorry, but no magic skull AI. Harry writes his potion recipes down on paper like a normal person. This also explains why he doesn’t always have great potions on hand, he only knows how to do the ones he’s worked out so far. )
Edit: Also, if we want to have a clear magic vs technology divide, make magic unable to scale. Magic concentrates enormous power in a single person, but it can’t be done assembly-line style, so it’s impossible to have the equivalent of an industrial revolution.
One obvious limiter is inborn magic talent, but you don’t need to go that route.
Take luck charms. Say the amount of energy it takes to make a minor luck charm is about half the amount it takes to make a major luck charm, but a minor luck charm means you probably won’t stub your toe and a major luck charm means a dozen machine guns on full throttle can’t hit you. Wizards therefore make the max level of whatever magic item they’re capable of, rather than dividing their power to make a dozen at once. Magic can never be properly manufactured and distributed. It’s always a haves/have nots setup unless basically everyone has magic, and there’s no incentive for the magic users to open schools for everyone and try to get to this point because then everyone else has the magic and doesn’t need them for it.
A society could democratize magic, and such a society would probably do way better than the ones being assholes about it, but you can say the same thing about training ordinary people to fight, and plenty of societies chose otherwise. The magic flipping on and off makes it practically impossible, because the old guard setting the standards each time are a bunch of power-grubbing babymurderers living in constant fear of a peasant mob – but it’s always possible that one time, a set of the new supercharged wizards they’re afraid of might overthrow them and teach magic to everyone.