or option 3. Starfleet figuring out a way to get TMP nacelles to work on an Excelsior-variant ship in 2295 is a big difference from Starfleet doing the same thing in 2371.
I would think the "real" answer is actually a bit of all three, MOSTLY Option 1, but with some 2 and 3 in there.
It doesn’t make sense for the Frankenstein fleet to be that way by design. If Starfleet meant to create a Lego fleet, the esthetics of the ships would reflect that. They don’t.
This for sure, at least partly.
The kitbash ships are clearly something born more out of necessity. It's not the say that they are just old bits of ships slapped together, but they are also not
ideal.
The kitbash fleet was certainly built out of necessity, or perhaps just a bit of efficiency, more likely a little bit of both.
The previous 3 option deal...
1: Yes, there's no problem with a bunch of Starfleet ships being modular in nature. We "know" that Starfleet does this, from more background information (things like bridge modules and what not). I don't see any issue with that applying to more parts. Sometimes, they just end up assembled in unconvential ways that might be "ugly", but they work.
2: I don't think it's an "unexplained" reason... things happen to ships. If you end up with an otherwise perfectly good ship that got cut in half by a space amoeba, some of the parts are still perfectly usable. Why waste them, especially if many of them were built to be modular? If a ship is destroyed, but the warp nacelles are still fully intact, why not use them?
3: I think just saying "they somehow figured out how to use them" is the wrong way to look at them. Modular is modular, even if it's not ideal. There's not particular reason why a newer hull would be incompatible with an older warp drive. Sure it would be better if they popped a newer warp drive into it, but if they're in a situation where they have a few scuttled ships and they have a saucer, stardrive, and nacelles from three different ships... but those sections were all designed to be at least semi-modular... whelp, looks like you got 1 functioning "new" ship that required fairly minor alterations to work.