Hi there, I've been wondered how it's possible to choose one building and the other are no more available.
Here's an example from SS 6.4. They changes the Religious Orders from guilds to buildings. Then you could choose between the Templar Chapter house and the Hospitaller Chapter House.

Let say you choose the Templar, when you start building, the Hospitaller is no more available to construct in this settlement!!

Now, hopefully you understand what I mean. Let explain the steps. Really easy, you only need to play with the EDB!!

1)Find your building
2)At the end of the selected building add this entry:

and not building_present building_name

What's in blue is the name of the building that you don't want to be available when you build the selected building.

For example:

Spoiler Alert, click show to read: 
st_johns_minor_ch requires factions { england, france, scotland, denmark, norway, hungary, poland, papal_states, milan, sicily, venice, } and hidden_resource st_johns_chapter_house and not building_present templars_chapter_house

What's in blue is the selected building. In red is the building that will be no more available to the settlement when the selected building is constructed.

3)Save it and play!!

Hope this will help you . I thanks Meneth to pointing me out this possibility