FASA's TNG ships were always a little weird, even by their standards, but I sometimes wonder if perhaps they were meant to represent a new form of warp geometry?
Whatever the in-universe rationale, both the practical reason and the end result of the FASA approach are fairly evident. Namely, using copy-paste saucers and nacelles and then applying an original secondary hull will necessarily result in very large secondary hulls in comparison with saucers!
The FASA ships are apparently first drawn in side view, and you can't fit much of original work in there unless you draw "around" the nacelles, that is, above, below, forward and aft of them; anything going in between the two nacelles is lost to the side view. Compare this to the actual models used in shooting the shows and movies, which are 3D shapes first and foremost and typically have all the interesting bits between the nacelles, hidden in side view. After all, on screen the ships are virtually never
shown from the side, because that would look too much like Flash Gordon.
This is why we get "tall ships" like the
Keith or the
Bader or the
Durrett in FASA, but seldom on screen...
As for diversity of types, at all stages of naval history there has been a drive to minimize the number of designs. This is simple economy, although the exact variables forcing the economy vary with the era. Today, multimission ships rather than specialist designs are built because navies want fewer keels overall, the key variable now being crew salaries, the other being the expenses of idling a specialist vessel when her specialist skills are not acutely needed. Just a bit over a century ago, crews were a completely irrelevant factor, there being an endless supply of seamen of whom few special skills were required; idling cost virtually nothing, too, and ships rotted away at the same rate regardless of whether they were active or passive. The pressure towards fewer types earlier on came from things like steel shortage, lack of certainty about the threat environment, shortage of coal, shortage of timber, etc. etc.
Starfleet probably doesn't care about crew expenses: it's got billions of well-educated volunteers, and its ships are lavishly provided with crew comforts with no hint of holding back. Starfleet is unlikely to suffer from shortages of shipbuilding materials or facilities, either. And we have seen ships idled for decades or perhaps centuries and then rather easily reactivated. But we know Starfleet is permanently short on ships nevertheless, in all eras and all episodes and movies. Perhaps this is because there isn't enough dilithium for more than a certain number of ships, even if the Federation could complete thousands of times more keels? Whatever the key variable, the shortage would have the natural result of gravitating Starfleet towards generalist rather than specialist ships: a minesweeper would be a wasteful investment if she couldn't double as a surveyor and a patrol vessel.
(Oh, and regarding submarine tenders, I could very well see Starfleet or its Romulan counterpart employing a dedicated cloakship support vessel in the TOS era, if cloakships back then were by necessity as cramped and slow as the ones seen. The rationale would be very much the same as for sub tenders today!)
Timo Saloniemi
The K'Mirra (Alliance) battlecruiser was a hybrid based on the Klingon 
