I don't think Bobby (the creator) cares one little bit about whatever ships any other person has.
The game doesn't revolve around the ships, so it shouldn't really matter. Those are his favorite 3 ships, it isn't any fetishization or anything like that.
As far as we know thee aren't any other ponies other than the CMC, so other ships aren't really relevant or even an issue.
And as for the C&D, there's hardly any reason for that to ever happen, Hasbro probably isn't going to care about an RPG Maker game that doesn't even have pony in the title! As far as I know they've only C&D'd two or three fan projects. Fighting is Magic was far too polished and was going to be at tournaments! Highly unlike;y