I want to make gunships be neutral when not used, but I can't do it. I don't understand where they are getting their Team value. Same applies for command walkers but that's not as important.

Which gunship ODF are you looking at? Rep_fly_gunship is flyer class and shouldn't have a team value. Rep_fly_gunship_sc is a commandflyer and will always have a team value since its a command post.

Maybe with some LUA coding you could check if there's anybody in it, and if not make it neutral? And then change it to either team 1 or 2 depending on which team owns it. I'm not sure if you're able to check one exact vehicle, but if there's only one of that vehicle class, it might be possible.