I go with the official line, that the main reactor is in the secondary hull, a.k.a. the engineering hull,
which feeds power out to the nacelles, which contain the warp coils and other doohickeys, which generates and regulates the warp field.
The thing to keep in mind is that whenever the threat to the ship was largely external, like some mad supercomputer has grabbed the ship and will blow her up unless Kirk does something down on the planet, like talk the computer into blowing itself up, the technobabble is all over the place, and oftentimes focuses on the obvious trait of the ship's power, those big nacelles.
when the ship itself is threatening to blow up and Scotty actually has to do
something to prevent this, we are almost always
presented with an internal m/a reactor.