The power generation is in the hull though, not the nacelles. Why shouldn't newer nacelles just as easily down-tune to work with older power generation?
What i'm thinking is that power generation/warp drive tend to go hand in hand, and warp drive would be the most complex system of anything. I'm generally thinking that a warp core/nacelles are a single system and that is something that can't (easily) be adjusted.
And even if you could hot-swap nacelles, I feel like an older warp core would just flat out of be incompatible with newer nacelles, while a newer warp core could still have backwards compatability.
The problem with this idea is that almost all the kitbashes we see are just... Excelsior and Constitution mash-ups put together in really odd ways. Just... deconstruct them and put them back together the right way round this time.
Yes and no. Constitution-style nacelles seem to the nacelle of choice for the later-23rd/early 24th century generation of starships, and seem to be damn near ubiquitous for the era. There's probably just... ALOT of them out there. So we see them most often.
If my web of theories is correct, there's a few reasons that make that make sense... if the Khitomer Accords put a limit on the creation of new warp cores, if the Federation was on a somewhat cold war footing and producing a ton of ships/parts pre-Khitomer... it makes sense Constitution and Excelsior parts would be common, even a century later. If there's a limit imposed on new warp cores, it's in their best interest to keep the pre-treaty ones they have active, even if that means jury-rigging into them a new ship.
From an in-universe perspective, they did not just put them together in the normal way so there's a reason WHY... I go with the easiest possible answer of they just didn't have ALL of the parts needed when building these ships, and they were trying to build them quickly. They had like, 50% of an Excelsior, 30% of a Constitution, and 20% of newer parts that they cobbled together to make a new ship. If they had all the parts for one of them, they would just slap them together.
And, now, rereading the thread, I see the perils of leaping into a conversation mid-stream, I only saw the part about small-run and bespoke designs before, not the suggestion that they were built from stock components destined for other ship types. I have no problem imagining the Centaur or the Raging Queen (with rescaled nacelles) were legitimate turn-of-the-century designs that just weren't built in the same numbers as plain old Excelsiors (but, then, was anything?).
I think there's certainly room for both. Sure some designs work just fine as their own thing, like the Centaur. No reason that can't be a purpose designed ship.