Regarding the neck:
I would say then that the existence of a neck in general is, as you said, for "enabling a more efficient layout combination of engines + secondary hull", but the fact that they are so narrow is because of the benefits that has for the warp field geometry. Otherwise they would have been built wider and therefore stronger from the beginning (say, as wide as the engineering hull itself).
I agree on the heavy nacelles as the main reason for their rarity with the other points as further reason not to build them. The only things speaking for them are their very high endurance and dash speed.
Maybe the weight problem is also another reason against 3-nacelled ships.
I just realized that the spindly design of the neck (together with the nacelle pylons) could be all about saving weight. They're only as strong as is needed, and more combat-oriented ships have another, more rugged design altogether.