Four rooms in the saucer would explain the two distinct shapes and standards of equip. That is, they'd account for the enlarged set with the food dispenser and the viewscreen, and for the sometimes varying door colors - the slightly mobile control console might best be explained as indeed being unattached to the floor, except by some sort of reliable magnetics. Remember how we sometimes see Kirk's command chair pedestal lifted from the floor, too, or how the big "transformer" thingamablobs at Engineering appear to wander about?
We might still want to believe in additional (cargo?) transporters in the secondary hull, too - to go with the Deck 14 reference when Simon van Gelder is beamed up in "Dagger of the Mind". Further believing in emergency evacuation transporters and the like wouldn't be a big step, either.
But we have seen several times that a central resource can get damaged or otherwise be lost, preventing use of any and all transporter rooms. Some sort of central control then exists across all the possible platforms. Yet active, positive control is not necessarily required, as it's not implied anywhere - not even in the total evacuation events we see or hear about ("This Side of Paradise", "Doomsday Machine"). Instead, each platform might be operated via its dedicated console, which as we witness (say, "Let That Be Your Last Illegal Beamout") can be set on automatic for the last person to leave.
TOS never seems to feature explicit remote use of transporters, although "Tholian Web" comes close with Spock ordering "ready to transport on my order" without pressing the intercom button, as if somebody on the bridge were to be the one to execute the order. Of course, Spock is never heard giving the order! We probably have to pretend it was "lost in editing", i.e. happened when the camera was doing something else. Perhaps we lost Spock's pressing of the intercom button, too? Or perhaps Uhura relayed the order to the transporter operator down below?
If not, though, this rather anomalous case could serve as our proof for centralized command of all transporters.
Timo Saloniemi