Hmm. I'm in the camp for accepting that there probably are dozens of ways to skin the warp propulsion cat, and that ENT, TOS, TMP and TNG might all have utilized engines that were subtly or grossly dissimilar, despite looking more or less the same to the outside.
OTOH, nothing about warp nacelle placement changed when antimatter reactors explicitly became internal to the secondary hull. And ejectable pods other than the nacelles seem to have been a feature of all the warp power and propulsion systems in all the shows and eras. "That Which Survives" especially seems to show Scotty toiling on a single matter-antimatter reaction chamber that involves an ejectable magnetic bottle arrangement.
Doesn't mean there wasn't antimatter flowing in the nacelles, too. But the reference to a single reaction chamber makes it a bit unlikely that there would have been much mixing going on up there. Unless we speculate that Losira was only able to sabotage one reaction chamber out of many, and was kind enough to sabotage the one in the engineering hull (so that Scotty could save the day) - or perhaps cruel enough to sabotage that one, instead of the more easily jettisonable nacelle ones?
It doesn't sound as if Losira actually sabotaged the m/am intermix system, tho. Spock just suggested this as a practical location for cutting the fuel flow to the engines which couldn't otherwise be shut down, thanks to Losira's sabotage. Perhaps the m/am chamber mixes the fuel but then has it delivered to the nacelles for the actual power generation? Doesn't make much sense to mix (or, as Scotty says, "integrate") matter and antimatter unless for power generation, tho. And a system that delivers energy from the integration unit to the nacelles is essentially what we have in TNG.