I will have to refute some of your points, please don't take it personally.
I do not, please do not take my refutaton of your refutation personally.
Voyager did have a saucer. True it was more triangular, but it was both longer and wider than it was deep. The Long Range Science Vessle is deeper than it is wide, as such it looses the clearly defined saucer section.
Um... a saucer is round, that is why it is called a saucer. Because it resembles a saucer. An arrowhead, no matter how flat or wide it may be, does not resemble a saucer.
The Voyager represented a considerable jump in Star Trek ship design, because while it had a primary and secondary hull, and paired nacelles, like the Enterprise, it was the first to replace the saucer with a more pointed, aggressive design. By contrast, the flow of the ship itself became more curved and aerodynamic, taking on a shape derived from the way the Galaxy-class Enterprise had been curved.
There is debate as to whether the Miranda's roll bar was for weapons or the engineering section (I think it was both). The Nebula does indeed have an engineering section which is the same as the Galaxy. In fact, the Nebula really does have the same mass and volume, it is just more compact and has a smaller surface area compared to the Galaxy, but I digress. The Saber, Akira, Norway, Steamrunner and NX were created after Rodenberry's death. They do have engineering sections. The pyloins and pods consitute the engineering section. Both the Daeleus and Olypmic do indeed also have engineering sections as well.
By "engineering hull", I was talking about the third body that descends down from the main body of the primary hull. I am not saying anything about some portion of the hull which is sectioned off for engineering purposes, and I don't think that's even relevant. I am talking about the asthetic sense of the original TOS Enterprise, which balances the upper warp nacelles with the engineering hull underneath. The Galaxy, Sovreign, and Excelsior class Enterprises all had such a secondary hull, just like their predecessor, as does the Voyager. The NX Enterprise, Miranda and Akira have only a primary hull with nacelles attached directly to it.
The Nebula does have a secondary hull, but it is tucked under the saucer and the engines descend down beside it instead of up from it, and the "pod" on top of the hull extends from it as well. So it is not as prominent a part of the design as it is on the vessels that carry the Enterprise name. Its appearance is quite more clearly descended from the Miranda and it's "roll bar", which is itself a derivation of the Motion Picture version of the Enterprise, with its nacelles removed and placed under the saucer hull.
As for the three nacelles, that is clearly against what Rodenberry advised.
The Galaxy Dreadnaught is the ONLY place three nacelles appears in the canon. And I like the explanation given that the Galaxy class warp pods (meaning those on the Nebula as well) have two warp cores, making them effectively two warp nacelles stuck together. So the assertion that warp nacelles be in pairs is not broken, there are three pairs, and they are in clear view of each other. You're probably right about the warp envelope being irregular, but likely the idea was to increase reduncancy, and allow warp flight if one pod was destroyed. The other two (or one, on the Galaxy) could be shut down and one pod used to achieve warp.
This explanation has been applied to the one nacelle designs in "Best of Both Worlds", but I consider it just as likely that as wreckage the ships simply lost their second nacelle. We can't be sure of the configuration of a wrecked ship. So really, we've only seen one ship with an odd number of nacelles actually in operation in the canon, and that was a future ship that might be operating using technology that simply wasn't available for most of the series.
That leaves four warp nacelles, which does not in any way invalidate Roddenberry's criteria that "warp nacelles come in pairs". They DO come in pairs, a PAIR of pairs. This has appeared several times in canon, the closely placed, upper and lower nacelles of the Constellation class Stargazer, as well as the more widely spaced and balanced Cheyenne and Prometheus, both the ship classes found here in this game. Presumably, the Nebula can also replace its upper pod with a PAIR of nacelles, and so I suppose it is possible that the DSSV's lower pod could be replaced with a pair of nacelles as well, or even a unified paired nacelle pod, like on the Stargazer or the theoretical Galaxy pod.