Would it work to create a single hidden building with a +1% gold modifier, then add 63 instances of this building?
Yes, it would; there's usually no reason to have multiple denominations when you can just stack more instances of a 1% or +1 shift. My mods use stackable hidden buildings for this, with SetNumRealBuildings, except that I mostly use flat +1 increases instead of percentages (with the sole exception being gold in my "Head Start" mechanism for late-era starts). I primarily use this mechanism for my Priest and Empath specialists' Happiness boost, but I've also done this for other yields to handle other temporary bonuses (like the Seasons focus in the Mythology mod, where it rotates which two yields the shrine boosts depending on the turn number). It's worked very well.
The first thing I'd suggest is modding CityView.lua to hide these buildings. In my mod, any building with the <NoLimit> flag set for its building class is hidden automatically, although I could also toss a Cost check in there as well. If you don't, then the buildings will be shown in the city view; this wouldn't be terrible, of course, but the UI doesn't display how many instances of a building exist, so you wouldn't be able to tell the difference between 1 copy and 63 copies in a city. (I also drop these buildings from the Civilopedia.)
As to how it works in practice? The AI occasionally makes mistakes with it. Because it's a building, the AI will take the extra yield into account when deciding whether to build something, which is good, but it won't understand that that yield will be taken away a few turns later. So it might commit to building a World Wonder (which normally have a 50-turn cutoff, as in, if a city would take more than 50 turns to complete the wonder it won't even try to start it) in a city with a temporary production boost, and then it can't change its mind once that boost goes away and might be stuck on a 100-turn build action. Granted, you already run into this same thing with Golden Ages in the standard game, but if you're using this hidden building mechanism heavily, it might occur much more often.
But generally speaking, the AI handles it pretty well; at least, it's no worse than the AI handles anything else in this game.
Now, whether or not you'd want to use multiple types for each yield depends what exactly you're using it for. For instance, in my mods, I've got four things that can temporarily boost Happiness behind-the-scenes:
> Priest and Empath specialists
> The Head Start mechanism for late-era starts
> Researching the Transcendent Thought tech at the end of the Ascension tech tree
> Certain rare events can give your empire a permanent +1
At the moment, the first three are added together to determine how many copies of my +1 Happiness building I need to spawn in each city, and the fourth is handled separately. But I'm now looking at splitting the first type up further, because I'm trying to teach the AI how to handle Priests/Empaths, and for that, I need to know how many of them I'm using at any given moment. Being able to just count up instances of a building is MUCH more convenient than looping over all cities, looping over all buildings, and counting up the slots of that type. So creating two or three different building types with the same +1 Happiness effect is not a bad idea, if you need consistent bookkeeping for other reasons.