I've always gone with what Jefferies thought, that the nacelles contained powerful, dangerous
energies that needed kept away from the rest of the ship.
My own opinion is that the anti-matter containment tanks/modules would be THE dangerous things
to eject in event of emergency. The reactor itself, without antimatter involvement, would just be a inert hunk of metal.
I always envisioned the layout like this: A/M tank adjacent to the reactor, followed by some sort of
feed/distribution/modulation assembly, which then fed plasma to the coils, and to the rest of the ship.
With all the later "warp cores" and "warp plasma?", dialog, tech manual descriptions, etc, my opinion goes completely out the window.
Visually, the glowing exotic cool warp core sets look better than, well, tanks inside nacelles.