Sorry, I don't get your point here. Are you saying that because no character pointed at the two big glowing shafts located across several decks and monitored from main engineering and said "that's the intermix chamber, you know", that we don't know for sure if it is the intermix chamber? I think that's a little silly.
The intermix chamber is where the crystals are.
The central crystal chamber was never identified, though - that's correct. We don't know exactly where the crystals were located in the refit ship, or exactly what purpose that reactor room served. However it is logical to infer that the room does house the crystals when we see the similar piece of equipment in The Voyage Home.
You're saying it's logical to compare Klingon technology and design and Star Fleet technology and design as being synonomous?
"YET we know that the crystals mediate the reaction of matter and anti-matter so why would the chamber be in another room?"
Quite. It's another design element introduced in the second movie that doesn't really make any sense and was clearly added for the narrative need to provide Spock with a "sealed" room in which to venture to fix the warp drive and succumb to radiation poisoning. My theory is that perhaps matter and anti-matter are first introduced to the Crystals in the reactor room and the resultant plasma is siphoned away into the intermix chamber where it is further 'processed' in some way. But it is admittedly a flimsy theory based on a supposition, caused by a frankly baffling design detail.
The only problem with the room is if one insist that is where the crystals were housed for a subatomic reaction. Looks like a plasma valve to me.
The schematic you've provided there actually raises more questions (and is, I believe, not produced by official sources but by a fan). For one thing, although the intermix shaft connects with the deflection crystal, it also seems to be bypassed by what looks like another horizontal intermix shaft, albeit a short one. Which raises the question - if there is a second horizontal shaft which connects directly to the impulse engines, why is there a need for the deflection crystal at all? It's also interesting to note that there is no area for deuterium storage specified - unless the area at the bottom of the vertical shaft contains both matter and anti-matter, which would be acceptable as this M/ARA system does not appear to operate using the "injected at opposite ends" method (hence the lack of a centrally-positioned crystal in the shaft itself).
This was a buyable package under paramount for The Undiscovered Country by [SIZE=1]David Schmidt for the 25th ann. addition.U[/SIZE]
It was copyrighted therefore officially endorsed but of course not official canon.
The Impulse Deflection Crystal:
Like Warp Drive the Impulse Engines are a type of field propulsion system. The Fusion reactor ignites the matter and the energy from that reaction is then colaspsed into spatial disturbance that radiates out from the reactor. Only certain materials react with the impulse wave. Impulse Drive coils can be used to repel or to be attracted to the distortion wave
Residual plasma is flushed to the rear in the Impulse manifold on the exterior of the ship.
The Deflection Crystal cancels out residual wave activity on the opposite side of the drive coils.
The Additional Conduit routed to the impulse drive coils and manifold as seen in the illistration allows the coils to be powered by warp plasma or for the core to flushed incase the core is scrammed mid-reaction