I'm not aware of any instance of a real-world Star Trek starship designer caring one iota about fictional "stats" dreamed up by fans. There are cases where such "serious" designers have created their own set of stats for merchandise or just plain fun, but those would by default be compatible with the observed Trek designs, not needing any retconning.
The cases mentioned above where the specifics of a Starfleet vessel have changed have been relatively blatant, and could always be interpreted as the particular ship or ship class receiving an upgrade, a downgrade or some other corrective modification.
There are more subtle cases, though: the TOS starship changing configuration between various shots is one case that cannot be explained as an in-universe modification. It might be rationalized as the starship possessing variable-geometry elements, though...
Another category of subtle cases is when ships originally portrayed by physical models suddenly start being portrayed by CGI models that differ in detail or in major features. The Dominion medium warship underwent such changes - but since we never followed the adventures of any single such warship, we can always argue that the different ship styles we saw represented different, parallel subclasses, not modifications and remodifications of specific vessels.
Ideally, other Galaxy class ships would receive the extra phaser banks upgrades, but prior and for the duration of the Dominion war, most galaxy class ships did not have them per on-screen visual evidence (although SF had ample amount of time to implement them).
Those phasers may have turned out to have been a misstep and a disappointment, because we later ("Tears of the Prophets") saw a
Galaxy class starship named
Venture that no longer had the extra phasers.
I think there are 2 version of the Ambassador class ... one with more exposed Bussard collectors, and the more up-to date version that has extensions on the top and bottom of the collectors like the Galaxy class (and possibly the inclusion of a ventral phaser array).
The two versions also have their engines and hulls attached in a subtly different manner. Such a change would represent a rather massive refit, but fortunately we don't really see any single individual
Ambassador class ship exhibit both configurations. So apparently there were two models built by Starfleet, the latter one installing the hulls and engines in a more optimal manner (in addition to altering the ramscoops, lifeboats, stern shapes etc. and possibly adding the ventral strip).
This pales in comparison with the refit done on the E-E, though. Forget about the added weapons or reshaped pylons or whatnot: any decent dockyard could swap the respective components and effect the changes. But the secondary hull curves were also subtly altered - and this would mean in in-universe terms that the entire hull was torn down and then rebuilt! That's massive - way more laborious than, say, installing a third nacelle or a triangular primary hull.
I doubt this was done on every
Sovereign, then. Perhaps the E-E suffered catastrophic damage to her secondary hull and had to be completely rebuilt between ST:INS and ST:NEM?
Timo Saloniemi