AmbassadorKosh is referring to "The Apple":
KIRK: Then use your imagination. Tie every ounce of power the ship has into the impulse engines. Discard the warp drive nacelles if you have to, and crack out of there with the main section, but get that ship out of there!
The reason Kirk tells him this is because at that point the antimatter pods were rendered inert meaning no warp drive and only the impulse engines (in the primary hull) resisting the tractor beam. It seemed logical to dump the massive engineering section and pods to lessen the mass to escape.
That doesn't mean you couldn't fly the ship from the Engineering hull though. We've seen "Is There In Truth No Beauty" and "I, Mudd" that the ship can be flown from Engineering if the appropriate settings are changed.