Well, look at TOS Enterprise vs. TMP Enterprise. As Decker put it "This is an almost entirely new Enterprise." Look at the massive upgrades it had, not just the saucer but the secondary hull and nacelles. What was original? Maybe some of the framework and a few bolts? It would have made more sense just to build a new ship. I'm guessing that some of the other Constitution class ships also had the same massive re-fit (I doubt the Enterprise-A was a brand new ship considering its short life before being decommissioned.) I guess different people will create their own in-universe explanation when things don't make sense and there's nothing wrong with that at all!