First a question:
Can the flying units be attacked by units on the ground?

The skeleton scale might be the reason it wont go between the gates as the engine might be able to tell that the skeleton cant fit between the gates - I believe this is how the game knows siege engines cant fit because there is no collision data for these units unlike buildings. Cant you change the speed of the mount somewhere else instead of changing the unit scale (descr_units.txt or export something or whatever) to counter the fact that the skeleton is smaller.

This looks good - keep it up. There was loads of talk about doing this sort of thing but all attempts have always been flawed in some way - mainly the attacking from the ground part.

What you may want to research into is making your own animations as this will give you the flexibility to build whatever flying fantasy beast you want. This also allows you to vary the height of the unit so you can make it dive down to attack enemies and such.

Personally I believe this is possible even if it will be tough to pull off. Keep it up