To me, it's an Occam's Razor thing. There was a ship called Enterprise, then it's blown up. So its crew are assigned a new ship. Also called Enterprise. Its a new Enterprise. If it was simply a refit, why wouldn't they call it by its old name? They didn't change the name of the previous Enterprise in TMP, despite its extensive refit.
I mean, okay, there's nothing onscreen to say one way or the other but the other explanations seem awfully convoluted to me. And TFF certainly seems to support the idea that it's a new ship, with all the associated teething problems.