Join aircraft transport units with other units

I believe they do. At least they used to. You can stack airplanes with naval stacks or land stacks and any damage the stack receives is distributed among the whole stack, particularly to any infantry whether at sea or on land.

For a long time, the air units had to travese alone, seperated from any other unit stacks in the water. That changed only a few updates ago to where they are now inclusive to any chosen.
Stacking with naval is always a smart idea, if not simply for the protection each offer the other during movement, but also for the stable morale factor of stacked land units.

HannibalBarca1

You can stack airplanes with naval stacks or land stacks

Currently an aircraft transport doesn't seem to stack with land unit stacks.

Planes on naval transport ships don't stack with regular ships either.

I think if the railgun can go by ship, air transports have to as well, since it's easier to transport than a railgun. And in the case of ground movement, it's completely logical that the other units could escort the aircraft transports just like they do with the railgun.