Being able to capture enemy ship building units that are not of your own (sub)faction would become game breaking. Building ships that are not of your faction would put other players at a tremendous disadvantage since you can produce ships for your fleet (that are not of your faction) reliably.
I feel as though one should only acquire ships not of their own faction by boarding the ship one so desires. If anything, an enemy Frigate Factory should produce ships for you, but maybe at a quarter of the regular speed and build your faction's ships. Advent Frigate Factories are not geared to make TEC ships, for example.
On the other hand, if they add in some way for the other two factions to also capture enemy ships and modules (maybe not the same way, but the same result), it could add a whole new dimension to the game, rather than being game-breaking.
Example: the Advent could have a capship that can capture enemy ships by directing a "culture beam" at the ship, completely enveloping their communications and (okay how unbelievably sci-fi do we want to make this?) altering time so that they perceive time at a faster rate, thus they spend several months being brainwashed in Advent culture in a matter of seconds, and come out of the "beam" completely devoted to the Advent.
Not sure what the V's could do, but you get the idea. Let everyone cap everyone else's stuff, and sooner or later everyone's using a mixed bag of technology. You could even build other factions' starbase constructors and thereby produce even more ships using the construction facilities on the starbase! 