Do Star Trek refits make sense when even the external structure changes?
Short answerYes; for a spacecraft, volume, time, and resources are the main constraints, and a post-scarcity society can support much more extensive rebuilding than a modern navy.
NotesThe prompt notes that some Star Trek refits alter nearly every visible part of a ship while retaining the language of refitting rather than rebuilding. A spacecraft is free of many constraints imposed by waterborne hulls and gravity-bound dockyards. The practical limits become space, time, and resources. In a society with fewer financial constraints, an exceptionally extensive reconstruction can remain a plausible fleet practice even if the label sounds conservative by present naval standards.