^These cases of refit may have been instances of high profile politics trumping practicality. Of course, production wise it was a "have their cake and eat it too" compromise. They wanted it to be the same ship from TOS, but wanted freedom to update the design for the big screen. This idea would have been more credible with the initial Phase II design, but after all the changes by Andy Probert, it became much harder to see as the same ship. Likely the reason we didn't see that concept used much after is that Trek never had such a huge leap in quality and budget for effects as TOS to TMP. And when such changes did happen, they were with different ships or locations. Probably the next closest is probably Nemesis to Star Trek 2009, but we have an alternate reality to explain the differences.
Though internally, we do see lots of the Excelsiors, Oberths, and Mirandas sporting the "TNG" aesthetic inside. And with the warp speed effect using the Q-flash instead of the cartoons streaks suggest substantial changes to their warp systems.
In universe, one might suppose that in both the TMP and TNG timeframe, ENTERPRISE carries so much political weight that starfleet will undertake these impractical overhaul and space frame modifications simply so they can claim it is the same ship on paper. Though it is likely more cost effective (or as close to in a "moneyless" society) to simply build a new ship from ground up. We don't see much of the civilian sphere in TOS and TNG. But having one of those ship save earth from VGER and another save earth from the Borg, may have started a rabid fanaticism on Earth (the likes of which never seen on this website) that, short of her complete destruction, would not allow starfleet to ever retire the Enterprise. For all we know, one of the national holidays is Enterprise Day.