I really like this idea, as others have said, this reminds me of supreme commanders' nanolathes, the world devastators or whatever from star wars, and the carriers from Starcraft.
I like all of those, and I think the ability to easily build equivelants would be great! However, I must argue, I personally believe that all notable systems of a ship should require "controller" blocks to act as a lynch-pin, to make combat more manageable. I would also agree with fabricator systems able to be mounted on mobile ships.
I personally think ships magically appearing where you choose them to be docked, however, is pretty gay. I'd personally think you should have these slow-moving "laser cranes" let's call them, that would tractor-beam the constructed thing to wherever you wanted to move it to.
Ofc, to actually do that, it'd require the parent ship to stay in place. This'd be two-fold, it'd look completely badass, and it'd help balance a bit by requiring the ship to stop moving for quite a while.