Why can I not select a custom flying mount when doing most anything in bots?

[Croga]

Because you can use flying mounts as ground mounts

I agree. As said; I love seeing my mage carpet his way through BGs but I do think this is what the populace that started and supported this thread are talking about.
I don't see the issue; a Big Bronze Drake in a BG is awesome and awe-inspiring. Nothing to complain about to be honest.