I think the way it will work is that if you're in an area that has no flying, you'll go into travel form. If you are in an area that you can fly in, you'll go flight form. And if you're swimming, you'll go aquatic form. So all three forms can be used, just will depend on where you are. If you're in MoP lands but don't have the MoP flying, you'll go travel form. Once you get the flying there, you'll be able to go flight form. And with WoD having no flying, you'll be travel forming it most times
At least, that's how I think it will work.