If they wanna say the Connie retroactively now looks like the SNW/DSC Connie, sure go ahead. If they wanna use the TOS version, equally go ahead. But at least put the flag in the ground and say ‘this is what it is now’.
I don't know. I don't think it's necessary to pin down one specific visual over all others. Is the third movie set in a different "universe" or "timeline" just because Saavik didn't look exactly like Kirstie Alley anymore?
Of course not. Audiences suspended their disbelief as audiences have done for as long as theater has existed, even if the cast or art direction aren't 100% identical to other productions. As long as the ship is recognizably the Enterprise -- saucer, twin nacelles, etc -- we can read it as the same Enterprise, the same way we accepted that it was the same Saavik, just played by a different actress.
Granted, this may be my comic-book background speaking. Different artists draw Batman differently. Kelly Jones's Batman does not look exactly like Neal Adam's Batman or Gene Colan's Batman, etc. But that doesn't mean only one look is "canon" or that we're in a new "timeline" every time a different artist draws Batman.
Just different artistic interpretations.
Same with the Enterprise, Klingons, Kirk, Spock, etc.