Be it the "Refit" Enterprise, or -A, virtually all the plans I have seen indicate the Vertical Intermix Chamber (seen in the Main Engineering Scenes in TMP and TWOK, and a modified version seen in TUC) is shown to extend from the bottom of the secondary hull through the neck to the "Impulse Deflection Crystal."
Is there any real reason to assume it must actually travel that way? Is there any on-screen evidence to indicate that it indeed connects with the IDC, or is that simply an assumption that seems to have universally been agreed upon?
I am looking over any and all deck plans I can get my eyes upon, and every last one of them seems to show that, and while in theory it might make some sense, actually trying to fit it into the neck is problematic at best. Trying to fit the torpedo tubes around it is neigh-on impossible, not without making some very poor ergonomic choices (do you really want the crew manning the Torpedo bays to have to pass through the intermix chamber room at every shift change? Do you really want to have one of your handful of exernal docking ports (one third of the primary ingress/egress points in spacedock - assuming the saucer edge on p/s, the secondary hull port that was used in TMP and the Torpedo Bay port used in TWOK) lead to people and any stuff they are carrying pass through the intermix chamber room almost non-stop while in dock? (yes, I know the ports were never seen to have been used for such, but the point still stands, why have a port in a location that makes it difficult to get to the remainder of the ship from?
Additionally, trying to fit both a turbo-shaft and the intermix chamber into the neck makes things very tight in the front (no good way to route the turboshaft around to aft of the intermix chamber, as in the saucer it would end up in the impulse engines before it could reach the neck). Overall, it would be a much more functional ship for personnel to use if the intermix chamber did NOT go through the neck.