As I have immersed myself in Trek lore (real-world and in-universe) for almost as long as I have Star Wars and Transformers, let me take you back to first sources...
Jeffries was an aerospace engineer, and he had some things in mind when designing the Enterprise. No rocket flames coming out of the warp engines -- nothing so primitive to tie it to what would, in the future, likely be as far removed from whatever propulsive technology they actually had as DaVinci's designs are from actual helicopters. He did indeed speculate that the larger the ships, the more powerful the warping effect needed, and the farther away from the habitable volume the engines needed to be. Hence why smaller ships can have the warp engines tucked in close with no harm.
This, incidentally, is why I hate the Sabre and St(r)eamrunner classes.
As for the line-of-sight stuff... *sigh* "Roddenberry's Rules of Starship Design" came about in the early '80s to discredit and render null Franz Joseph's new ship designs in the Star Fleet Technical Manual he published -- with Roddenberry's enthusiastic blessing -- in the '70s. Gene had asked FJ to work with him on a new pilot he was doing, but they were from different worlds and what should have just been a minor communications breakdown devolved thanks to their respective egos and stubbornness into never speaking again for the rest of their lives and Gene using every opportunity to smear FJ's work with Trek stuff. "Warp engines are always in pairs" was to nullify the single-nacelled Destroyer/Scout design as well as the three-nacelled Dreadnought; "Nacelles require at least 50% 'crosstalk' between the inboard field grilles" nullified the Transport; and the "Greater than 50% forward visibility" further hammered it home.
The other lasting damage comes from Gene insisting FASA and Mike Okuda not use FJ's work for Constitution class registry numbers. The only other resource out there was an issue of a fan magazine in which Greg Jein (one of the main model makers from the films through TNG into DS9) wrote an article wherein he used self-admitted "barely logical" methods to connect the known Constitution class ships in TOS with the list of registry numbers on Commodore Stone's office wall in the first-season episode "Court Martial". If not for this, the Constellation would have been the only Constitution with a <1700 registry number to sort out (honestly, I wish they'd at least done it as "1710", or even *gasp!* splurged for a second model kit so they had more options -- "1700" to make it the Constitution herself, maybe, or "1707", "1711", "1717", "1770", etc...).
This is why I hope they change the registry number to something like "10310" and place it in the "Lost Era" between 2293 and 2264.
--Jonah