@Arizal They are really not all unhistoric, the bonuses from Notre Dame and Taj Mahal for example are logical in my opinion. A big church giving Totf or a big Mausoleum prestige decay are not random modifiers. Just the 2 discussed here I feel like, why does a Foretress like castle allow you to administrate an Empire better? Or a fire temple in the mountains making your Canons hit harder then Napoleons? Giving access to these wonders to just everyone would be way worse...then seriously everyone would just rush the Alhambra or whatever as there is really no reason not to.
A bit late to answer you, but I reviewed most of them with a friend and you are right. Many bonuses kind of make sense. However, why cannot a church like Notre-Dame be built in Brussels? Or why a mourning sovereign can't build a temple for his wife elsewhere than in Agra? And I'm not talking about relocation. That's even stranger.
There are others absolutely ludicrous, like the Machu Pichu or Angkor Wat. What, just making those building was so difficult that they learnt how to permanently being more intelligent than the rest of the world? Why would having a city cast in rock allow anyone to have more diplomatic treaties?? (Petra)
One of the best ones might be Taj Mahal lvl 3. Remove the prestige decay bonus and you have a building that makes sense. A bit more prestige because you have a beautiful building. Harmandir Sahib seems similarly something that is realistic : they see a beautiful castle, so they are reminded of the power of the sovereign and won't try to find too hard against him (global autonomy reduction)
Hagia Sophia should probably be restricted to any big church/temple/mosque that sits in a province that has been converted. It's not the church that gives tolerance of heretics, it's the knowledge that the sultan let it be and didn't raze it to the ground.
Anyway, maybe the mechanic is salvageable, but as it stands there are many problems, just like the mercenaries introduced in Emperor. Too many bonuses don't make sense and there seems to be an insane power creep.