I know they recently changed the carrier modules but I still believe the spawns are predefined. As far as constructors, I am sure the Request Constructor feature still only makes the default design, if you obsolete that design the feature breaks. Although if you build the constructors yourself, I think it will pull built inactive constructors before making a shipyard build one.

It is pretty use to access the designs, or at least it was in the beta.  In the XML there is an option that hides the fighter designs from the ship list, you change that to show the designs and they will turn up in the shipyards.  This allows you to modify the design in terms of its equipment as long as you keep with the naming schema.  I did try switching out for a new ship template as well, but when loading a battle it didn't show the fighters in the list pre-battle and view battle just crashed the entire game.

I'm guessing if you wanted to have custom looking fighters you'd have to go into the XML and get it to call up a specific design, which means you can't change it in game.