I skimmed through the thread, so apologies if it's already been mentioned, but in the novelization of TMP which I read many many years ago, I am pretty sure (admittedly memory can play tricks?) Roddenberry mentions in his role as "official historian" that the move towards using the Enterprise insignia for all starships came only after the (apparently remarkable) successful end of its 5 year mission under Kirk's command. Production error or not, if I do remember correctly, Roddenberry himself seemed to think at that point that each ship previously had its own insignia.
(ON EDIT) Looks like my memory is faulty; skimmed through the preface and first chapter of my cooy of the novelization of TMP and don't find mention of the insignia. I know read that bit about the insignia being aligned after Kirk's 5 year mission a looong time ago, maybe in a "Best of Trek" anthology (in which case it would be pure fan speculation). Justman's memo notwithstanding, there is still clearly evidence to both support and discount the different insignias. Perhaps equal evidence (2 episodes each if I've counted correctly) for each side, since TOS just didn't give us that many glimpses of other starship crews. I'm one who goes by the multiple insignia notion. I think those of us who do are in good company.