On the "neck" issue, I remain rather agnostic on that. I do think it's a matter of subspace field geometry, but I think that's more to do with enabling a more efficient layout combination of engines + secondary hull. "Neckless" ships in general have very small engineering hulls, though streamlining in the case of the Intrepid
mean a slight difference there. (Their hull shape is still similar enough that they're "necked" designs).
The "off-plane" thing isn't really meant to imply other ships have trouble doing it as much as implying it's easier for a quad-nacelle ship to make rapid shifts in that direction. I'm probably going to remove it with a revision.
Quad-nacellers IMO basically give up sublight performance for warp performance. Nacelles are freaking heavy, they're by far the densest part of the ship. So tacking 4 of them onto a ship, no matter how great for warp maneuverability, endurance, or even dash speed, is an awful decision for the ship's mass balance in normal space operations. Also, The need to precisely attune their field geometry I think also makes them more vulnerable to damage.
lifeboat figures are actually a bit lazy. I need to go back and revise them. I do figure, though, that reducing lifeboat size and volume is one of the things that also raises usable payload volume.
For the shuttlepods, I meant Type 16, which in the TNGTM are an extended range version of the Type 15.
The Flyer-class is indeed a mass produced variant of the Delta Flyer II (as depicted on the Horne
from Over a Torrent Sea