So what I'm wondering, is who here is in the camp where the nacelles are not only part of the warp drive, but contain the volitile matter/antimatter reactors to power this huge and powerful ship? And what other lines from TOS substantiate this possibility?
Well, I think that everyone who's read anything I've written on here knows that I'm firmly in the "airplane design philosophy" for the TOS 1701.
Matt Jefferies was an aerospace guy, and he was thinking in terms of aircraft when he came up with the concepts for the Enterprise. In aircraft, engines are generally mounted remotely from the main fuselage, in external nacelles, typically suspended from the wings.
The engine burns fuel, and and this turns the turbines in the engines... which gives both propulsive energy and also allows mechanical energy to be tapped from the gearbox. The gearbox drives an AC generator which provides unprocessed electrical power as well as drives the hydraulic system's primary elements.
The electrical power as provided is unusable, however. It is sent to a complex array of rectifiers and inverters which provide a range of different forms of electrical power to various subsystems on the aircraft.
The Enterprise, as designed by Matt Jefferies, was intended to follow this model. Main Engineering, as designed by Matt Jefferies, was not intended to represent the main power generation system, but rather the location where the raw energy from the engines is transformed into a useable form.
It is true that in Elaan of Troius, comments were made which could be interpreted to mean that power generation occurred at Main Engineering. I'm not aware of any other place in the series where anything of this nature was said, however, and most of the series (and in particular, the items you mentioned) tend to agree with Jefferies' original intent.
So, I'm 100% in the "power generated in the engine nacelles, but converted into useable form in the secondary hull" camp.
No surprise there to anyone who's followed my work on the Enterprise, of course, huh?