Why not have a spacedock that scans and "beams up" say a runabout and then duplicates it? Obviously some materials can't be duplicated for example latinum, i'm not sure how many are used in starship design but then could probably copy and paste 80% complete shuttlecraft to their their hearts content, even duplicate defiants if they had mega -transporter-replicator copiers.
I was under the impression they do basically this, at Utopia Planitia and elsewhere.
But for that matter I don't like the idea that they can convert energy directly into matter, or even one element into another element. Because that's ridiculously hard and economically wasteful. I prefer to imagine that they're getting C, N, O, H, etc. from a bulk matter repository, which probably smells like and has the consistency of--and let's face it, is--sewage.
I do really like your notion that transporter tech can essentially copy people--but that's a technology that would have to be very
carefully approached from a dramatic standpoint in order to make effective stories out of.
Here's a truly new tech: holographic damage control. This involves holoemitters throughout the ship which are capable of patching EPS conduits, hull breaches, and exploding consoles. Due to the huge energy expenditures involved, eventually industrial replicators will have to put physical patches in place, but for the duration of combat, starships should have a significant advantage.