Nor has anything you said precludes it being a pre-refit version.
But my point was that it isn't a natural given
that the ship in the Museum is a pre-refit version. It could very well have been a case that the ship there was a later version rather than an early version, regardless of a holodeck simulation on the Enterprise
The interesting thing is that the Excelsior's bridge in STIII is a completely different bridge than what we saw in STVI, but it's the exact same ship. The same thing can be said for the Ent-A between STIV and STV. Or the completely different bridges of the Reliant, the Lantree, the Brattain and the Saratoga (Sisko's version), even though outwardly they are all Miranda class ships.
All this goes to show is that just because Scotty asked to see the bridge of the TOS Enterprise, and Picard recognized it as such, doesn't necessarily mean that the exact same inward or outward appearance of the vessel is the same Connie that's in the museum.
That's it in a nutshell, yes.