I hope you understand how hard it is to question their decisions with little information. That said, I’ve always been a fan of multiple systems in big homes. Yes, there is the maintenance but there is also back up heat and cooling if one goes down. It also provides the most even keel comfort throughout the home. I would probably ask about zoning the third room from one of the other 2 systems to cut it back from 3 if possible. The fans are really up to you. If you don’t need them you just shut them off but they may also be of great benefit if you do want them and it’s much cheaper and less intrusive to do it during construction rather than after the fact and you trying to match fans or replace all of them.