Indeed, since the one thing that we witness varying in otherwise identical ships is the engine placement, we would do well to speculate that there are definite advantages and disadvantages to having the engines "up" - and different, perhaps completely opposite advantages and disadvantages to having them "down".
One logical assumption would be to credit "engines up" with high top speed, because the various Enterprises
are quoted with speed records. "Engines down" might provide better cruise economy or something. And perhaps the fancy Intrepid
would have engines up for her reputed high top speed, but would relax them to the lower position at earliest opportunity because that consumes fewer resources?
Any modelmaker also knows how much more fragile the Enterprise
is in comparison with the Reliant
. Perhaps going for the fragility provides an advantage, but one Starfleet can't afford for the bulk of its forces, because fragility is bad for survivability and the maintaining of fleet strength. The "engines up" ships could all be silver bullet vessels for special applications, but this would by no means necessitate giving them the best and heaviest armament. Perhaps the special application is one less likely to involve weapons fire than the standard application for which the "engines down" ships are used.
Fans have come up with endless rationalizations for the differences in witnessed and dreamed-up ship classes, all of them pure speculation or at best conjecture. My personal set here:
is a fast Miranda
is a more survivable Constitution
, built in somewhat larger numbers and made more affordable by leaving some of the weaponry in an optional module. Otherwise, the two are built for the same generic purposes, and Starfleet continues to build such pairs of designs in all eras.
is the last hurrah of the technology of that era, before Excelsior
comes along. Because the old stuff isn't up to snuff and can't be made better
, Starfleet installs more
of it: four warp nacelles, two impulse assemblies, a thicker saucer with two topsides. The gapfiller isn't built in great numbers because Excelsior
is such a success, but its "all-frills", "bells, whistles and a church organ to boot" design gives it some longevity when at least part of it remains useful despite the passing of time.