If you or your players are concerned with balance, going with the reflavor could help ensure you won't be too far off. I for one would choose the reflavor, because it's less work.
Artificers don't really need a lot of reflavoring, just going the way the Alchemist subclass went.
They already have an experimental elixir feature and they can use spell slots to choose what they do. Keep all artificers as they are, but instead of preparing spells, they'll make draughts (up to the number of prepared spells) in the morning... Those are highly volatile and can't really be kept for long outside of lab conditions, explaining why they can't stockpile them and explaining why they don't have a definite allotment (since if they prepared, say, a cure wound bottle in the morning and cast Grease all day, they must explain in universe why there is no more cure wounds at the end of the day... Cantrips could be explained by mechanical device that can therefore be used at will, and maybe some experimental device (if you're uncomfortable with a potion to grow a patagium in a few seconds, you could have a single-use little device with a propeller expanding all its energy to let you fall not too fast and grappling you with its supertiny hands...)
Poring over the artificer list, there are very few spells I couldn't see easily reflavoring into potions you could ingest or pour over something to produce effect, mainly those with outlandish effect, like the Rope Trick one. Even Arcane Eye can be justified by taking hallucinogenic drugs giving an out of body experience... except it's really working.
The rules already encourage players to flavour their magic as mechanical... but doesn't harp on it. I'd totally explain the Arcane Jolt power of the Battlesmith as an experimental defibrillator drone (or, more thematically for a Victorian ambiance, a dingbot from the Heterodyne comic) , that can't be pushed too far out of fear of frying itself, but can help people in dire straits... or electrocute a foe) and so on.
If you want to link the story of your setting with character creation, you could use your factions as background for starting character and expand/modify the "spell list" based on each specialty, following the example set by Ravnica's guilds?
