Both of your points are good ones, and I agree. However, I still have a problem with Starfleet letting the Enterprise just sit in orbit for a protracted time period, perhaps years, before beginning the refit/rebuild process.
Do we know, though, that there was a "protracted time period"? I know many fans have tried various possible timelines. But from TMP, I believe the only references to the passage of time we have are Kirk's statement that he's spent "two and a half years as Chief of Starfleet Operations" and Scotty's statement that they've "just spent 18 months redesigning and refitting the Enterprise
." So that only leaves one year of definite time that the Enterprise
was not undergoing refit and also not under Kirk's command.
The producers of TMP went to a lot of trouble, too, to try and pretend that the crew hadn't aged much. It seems likely to me that they intended TMP to be 2.5 years after the conclusion of Kirk's five year mission, and for Decker to have taken command and begun the preparations for refit immediately after that mission.