Gliscor probably can't use the move because the flaps of skin they glide on don't leave any convenient place for their rider to put their legs around so it wouldn't be possible to sit astride one.
I'm not so sure about garchomp though. Its fin might kind of make it hard to ride on its back, but that's a pretty reaching excuse. And the idea that it would object to getting ridden on sounds pretty ridiculous considering hydreigon is perfectly fine with carrying people. It does look as if the only non-flying types that could use the move, fly in the 4th gen had levitate, excepting mew and arceus, so maybe the logic was that it shouldn't be able to Fly if it can't in any way fly (as in be ground proof). That wouldn't explain why it wasn't made able to use the move once the rule got apparently redacted in the 5th gen, but by the looks of it, the developers decided not to allow any pokémon that couldn't use fly in the 4th gen to do so in the 5th onward.
Speaking of fly, here's something kind of funny. While pidgey and spearow could always use the move, natu can't. You'd think that natu would likely have an easier time transporting someone with the aid of telekinesis or something, but nope, it can't get you anywhere. Maybe this was because its pokédex entry says it hops instead of flies, but that wouldn't explain why the doduo line can use the move just fine. Though interestingly enough, doduo's pokédex entries actually never say doduo is completely unable to fly. They only say it can't fly well, while natu apparently "has to hop".
So really, the only questions is how doduo and dodrio's too-small-to-be-seen wings let them fly better than natu's much proportionately larger ones. Even if doduo and dodrio actually jump and run instead of fly (which is how I've honestly always pictured it), natu can apparently jump higher than the height of a grown man, so it shouldn't have any more problems jumping out of reach for as long as a doduo can.
I guess really the transporting argument still stands though.