I think I have read Gene saying that, too. But, this was a long, long time ago, probably before TNG. Things change.
There are many single nacelle ships in Star Trek,
I doubt that manual was canon, (well, as much canon as star fleet battles is...)
Missing the point, point being the theoretical science behind something like warp drive, is valid
The position of the tech manuals and other "non-fiction" works for Trek is... vague.
They've never been declared non-cannon. They were authorized by Paramount. Gene considered them to be part of the background of Trek. The manuals were given to episode writers to use as guides.
Ronald Moore says they aren't canon. Viacom (that owns Paramount) Senior Director Harry Lang said he considers them canon in posts on Trek's official web forums.
That works about as well as a poorly documented, "Gene said at some point." Especially when Gene, being reasonable, occasionally changed his mind on things. It isnt' as if a 50 year old fictional property is going to remain particularly consistent. That a thing is canon and $3.50 will get you a cup of coffee.
Ah, well, that point was not at all clear.
The old Tech Manual not only had the single nacelle Scout and Destroyer class ships, but also a 3 nacelle Dreadnought class.
Yes the old ones did, but the next gen, and ds9 didn't
As I recall "Admiral" Riker's Enterprise, from the final TNG episode "All Good Things", was also a three nacelle design.

(Dungeons & Dragons)
Rulebook featuring "high magic" options, including a host of new spells.