off the top of my head i know baths, steles and mosques aren't capital only buildings and i dont see monopoly modifiers in there. also dont think the %bonuses to production for buildings made it in (progress) or the %cost reduction bonuses from forbidden palace/industry for example which serve the almost identical function. or the happiness modifiers, granted its probably a sufficiently fleshed out and intricate system that they make sense to have in place (although it is a bit easy to exploit through buying AI's luxuries, not just the spares but they often sell their only copy for a paltry price; 10-15gpt is nothing for them losing % bonus across the board and me gaining them). I dont see the rationalism opener, the science penalty reducer (effectively the same function again, but scaling up with # cities also), did opera houses make the list? I think there is more honestly we're missing but thats enough for now no? golden ages already had a sturdy inherent % bonus that came with them, not sure why so many more should be added in to that but at least theyre pretty brief until later in the game.
for the sake of argument you could even ignore modifiers from modern (maybe even industrial) era and onwards, I dont see a problem there because thats closing time but to my mind theres just no reason to have so many % bonuses before then, particularly in an instance like policies where you can have 2 players picking the same policy at the exact same time and getting different bonuses out of it, advantaging the person who was already in a better spot for no reason. its not like per city yields, having extra cities is another whole risk / reward / penalty system unto itself.
The incomplete list already shows there is definitely more than vanilla tho, and I think you know intuitively theyre kind of a bad thing as your first instinct was to say "hey, we have less than vanilla". I have no idea how im supposed to prove anything to you here though, even if i played out a common scenario that racks me up X amount of % bonuses by medieval, who's gonna say that X was "too much" or not. its a problematic function at its core, and while it has a place in the game for the sake of variety or where some system of scaling makes sense, I "feel" theyve definitely become too widespread / early and numerous because i recognize theyre a detriment to good balance.
BTW I think AI is keen on the fact of belief_world_church being pretty nuts, it goes quick. and mosques come out really poorly against synagogues.