The reason why the Repulse's registry is 2544 was because the model still had the Hood's original 2541 registry, and it was close enough (but not too close) for any viewer in 1987 to make out the difference.
If it makes you feel better I have the Hood listed as both 2541 and 42296 on my shiplist. However, I like your theory that the 2541 ship could be another Excelsior thanks to stock footage. In reality though, I find it hard to believe that every single time the Enterprise rendezvoused with an Excelsior, it was the exact same
Excelsior every time.