What were these guys at ILM trying to suggest?
One thing they seemed to be desperately trying to work into the designs (perhaps by decree from on high?) was variable geometry of some sort. The four-naceller appears to have swinging pylons for the X-Wing effect; this flat one with NCC-1404 has a telescoping midhull.
Should we "allow" these models to be examined in such detail that these concepts become evident? Swinging pylons are part and parcel of Starfleet design now, but the telescoping hull doesn't make much sense; perhaps we should accept that the "actual" ship in the far background at Wolf 359 no more looked exactly like this than another ship was named the Alka-Selsior.
Regarding primary hull separation, it does seem like it was a planned feature as far back as TOS, given Kirk's "crack out of there with the main section" remark in "The Apple."
Depending, of course, on what was considered to be the "main section" back then. Perhaps the saucer was just the "habitat section" or the "landing section"?