A warp engine swap might be among the more easily field-doable refits, what with these things being modular and at the ends of easily severed dangling bits and all. Perhaps phaser banks also are modular, with berths all around the saucers just waiting for the gun modules to be plugged in, and Starfleet at some point decided it could afford a few more on the hero ship.
The Klingon bridge thing is different, because we don't have to think the two rooms are the same. Both could coexist inside the tiny starship, for different purposes (Kruge's blue facility wasn't even called the Bridge in dialogue - only an unseen facility was, over the comms). We can't argue that the various nuEnterprises would be different ships, though.
Or perhaps we can, considering the rate at which nuKirk goes through those! It would appear extraordinary for him to keep a ship intact for more than two years...
Timo Saloniemi