If you already had 3 natural gyms and a sponsored gym is added you don’t lose any gyms. So there are 4
If one of those natural gyms is removed then no replacement gym appears as the 2 remaining natural and 1 sponsored gym make up the 3 max.
If you only have 2 gyms at the start and a sponsored gym is added that takes you to your max of 3 gyms no matter how many pokestops there are.
If in this case the sponsored gym later goes and you have the required number of Pokestops then a 3 rd natural gym Will appear.
My view is that I would prefer sponsored gyms and stops not to count but that’s a Pokémon Go decision.
This is not directly wayfarer related. 