Are you suggesting that Probert clearly had the idea all along that the shafts were just pipes for carrying plasma that had been generated down in a mix chamber at the bottom, and that no reaction was occurring in the shafts, so that when Roddenberry called the shafts "intermix chambers" and suggested matter/antimatter "annihilation" was happening inside them, that was just him going in a different creative direction than Probert? I don't think this is very plausible in terms of the production history (though of course you're free to use whatever headcanon you want for your project)--why would Probert call the place where the two shafts meet the "engine room" if the shafts were merely carrying energetic plasma that had been generated far below? In any modern vessel the "engine room" will be the place where the actual reactions generating kinetic energy are happening. And what about the quote from the lighting engineer Sam Nicholson that I posted (which was from a 1979 interview), are you supposing he made up the idea of the vertical shaft as a "reactor" himself, or got it exclusively from talking to Roddenberry?
I did a little more searching and found a
2005 interview with Probert where he makes clear he didn't have any very fixed idea about where the reactions were happening since he didn't know where the matter was actually coming from (he thought the 'keel at the bottom of the engineering hull' was just sending up antimatter through the shaft). He also says that the shaft leading upward from the engine room to the saucer was "trying to bring power up from the main engine room", which again seems to suggest the idea that power was being generated in the engine room (and in the question right before that he had been asked about the 'impulse deflection crystal', and said that the vertical shaft was supposed to 'channel energy from the main reactor, if you will, up into the crystal, which would deflect that energy into the impulse engine units', which combined with his next comment about how the shaft was meant to 'bring power up from the main engine room' seems to suggest he thought of the engine room as containing the 'main reactor').
He also says that the engine room was a mix of his own ideas and those of production designer Hal Michelson, it wasn't like he came up with a complete design for all the internal structure of the refit Enterprise that would be shown on camera and Michelson just built the sets to match those. But he does include a sketch he passed along showing roughly how he imagined the layout at one point in production (probably earlier than the previous drawing I posted since it doesn't match the movie as well), which has a "main deck" with the horizontal shafts (here a pair of them), an "intermix level" one deck below, and a "reactor level" one deck below that, all still in the top half of the secondary hull.
On the subject of Hal Michelson, the 1980 interview with him
here adds further support to the idea that multiple people in the production besides Roddenberry were thinking of the thing we saw onscreen as "the engine", not just conduits carrying plasma generated in an engine far below. On p. 13 of the interview he says:
He likewise refers to the two shafts as "a new kind of engine" of "limitless power" on p. 42 of
this 1980 Starlog article.