I don't think it does work - the primary hull, for one, is an entirely different shape. It would have to be the broom analogy Matalas gave to justify his insistence that the Stargazer WAS a refit and not, as all other evidence suggests (and Memory Alpha agrees) an entirely new ship.
Actally, the 25th century Stargazer seems like a relatively modern upgrade on the 23rd century Stargazer (constellation class).
The basic design is there. It has a saucer and 4 nacelles which connect at the back. Personally, I find the 25th century Stargazer to be a bit too fat on the behind and a bit too blocky for my taste... I would have preferred something similar to the Prometheus (design wise) to be the modern take of the Stargazer.
Its possible that SF harvested the original Stargazer for its raw materials and used them to remake it into the modern Constellation class. Replicators and transporters could do it in tandem.
Similarly, SF could have done the same when they refitted the original TOS Enterprise into the one saw in the movie.
Same ship, but it WAS restructured in many aspects.
In effect, it turned out (probably) to be a largely new ship for that massive refit.
I wouldn't be surprised if the same thing happened here. Only in the case of the Stargazer, the change was more extreme due to larger passage of time and more advances in technology.
ST: DISCO implied the USS Thikov may have been the same Thikov that existed since the 23rd century... just heavily upgraded/refit over time.
And given the fact it was a seed vault ship meant to protect seed samples from the galaxy, it would make sense it would be at a (usually) undisclosed positions in space and getting refitted over time.
Once a vessel reaches say the first 40 or 50 years or active service, its design structure probably starts undergoing visible changes to keep it on par with modern ships (naturally internal hw would be upgraded as well).
And the actual frame and underlying superstructure of the ship could be 'refreshed' with repliactors and transporters every 50 odd years if the stress accummulated enough to the point to warrant it. So in that case, you wouldn't really touch the rest of the ship (or it could be done simultaneously, if its time for the hw to be upgraded), just disaseemble bits of the old frame in the matter stream, reform it into same thing, but brand new, and beam it back into place.
Is it, though? It seems pretty clearly a plausible 'refit' of the Shangri-La class, see the gold ship models. That would better explain a 25th century makeover for the now-canon Shangri-La than either a totally new ship or an impossible refit of the Luna class Titan. It looks basically *nothing* like the Constitution II class. The only design feature in common is the front portion of the saucer section, which is shared with the Miranda and, rather obviously given said ship models, the Shangri-La. There is no way this design should be anything but the Shangri-La II class. It's only 'Neo-Constitution' or 'Constitution III' class because Matalas thinks it looks like his favourite Trek ship.
The dialogue between Picard, Riker and new captain of the Titan-A describes the ship as Neo Constitution in the first episode of Picard S3.
I agree that it works better as a 25th century refit of the Shangri-La class, but in fairness, the only thing that's mostly different are the nacelles and some changes to the secondary hull in addition to some phaser strips to the saucer?
23rd century design theme would have likely been phased out entirely by this point in time and the saucer would end up being more in Sovereign style or Stargazer (25th century version) like.
This would mean, no ball turrets, full phaser strips across the saucer, and various other 23rd century identifiable hallmarks.
Unless more radical design changes came about in the later part of the 25th century that would completely change the look of the ship but keep overall design philosophy (I say this because in early Season 3 of DISCO, captain Nyonte suggested that Disco, due to its mettalurty, may have been from a period of 23rd to 25th century - suggesting that if same ship designs persisted past that point, more radical changes to the hull geometry would have taken place in the 26th century to those designs to keep them on par with other ships (in the meantime, ships made and designed in the 23rd century would receive some changes to overall external look of the ship, which could be more extreme depending on which design they focused more efforts on - perhaps the 25th century Stargazer version)?
I'm just speculating here obviously, but the Neo Constitution line comes from on-screen dialogue.