So, with Steve's hint in one of the bug threads, I figured the currently proper way to "launch" fighters.
In the "Naval Organization" window, select the fleet on the left side (after you've already landed & assigned fighters to their mothership), then look at the "Ship List" on the right side. Mass selecting of ships works in this list, so you can easily select the fighters you need and then press the Detach button to "launch" them.
Now fighter fleet targeting mothership's fleet should have "Land on Assigned Mothership" order, without the need to assign them again.
There's a bug with deployment clock going into negative at the moment though, so beware (not sure what problems it may cause, but it's not great obviously). Also, "Join as Sub-Fleet" does not land the fighters, so don't try that either.