I concur but the engineering deck plans I'm currently finalizing suggest the cargo transporter not to be lower than Deck 14 (one deck lower we're running out of space). I'd say it's the same one as the one in "The Enemy Within" ("gathering specimen") were the engineering panel was added within the year before "Dagger of the Mind".
Sounds like an excellent idea. Incidentally, Shane Johnson, channeling Andy Probert, places the cargo transporters of the refitted ship on the second-lowest possible deck as well - Deck 19 at the floor level of the giant cargo hold. I'm not sure about your deck numbering and layout scheme, though...
Why would the decontamination system in "Naked Now" be unique? It rather seems that the situation
was fairly unique: our landing party discovered a reason to believe they had been contaminated, namely, something had resulted in the deaths of the people below and might be speculated to have been a contaminant. And they had some confidence that the contamination had not yet led to an infection, as they wore (partially) protective gear.
In episodes like "Enemy Within", danger from the contamination is not suspected; a change of clothes is the apparent standard way to deal with soiled coveralls. And in most episodes involving a landing party stumbling onto an environment riddled with an obvious disease or poison, lack of protective clothing in turn means the decontamination procedure would be insufficient. Apparently, and thankfully, the TOS decon system is different from the later TNG biofilter that routinely deals with (known) diseases and contaminants that might have been digested or otherwise absorbed into the body already.
I'm not sure of the virtues of dispersing the transporter rooms. "Enemy Within" teaches us the system has extremely centralized resources. And while "Doomsday Machine" involves transporter evacuation, "This Side of Paradise" suggests such a procedure is indeed time-consuming and impractical; avoidance of queues doesn't seem to be high on Starfleet's list of priorities.
On the idea of identifiable transporter rooms, what we witness seems awfully half-baked for the application. Surely outright signs saying "Transporter Room 3" or, say, color-coded consoles would be preferable to subtle differences in decor? A clustered transporter room arrangement would make identification fairly irrelevant anyway: no matter which room you use to beam aboard, you are going to exit into a corridor where you can easily spot the briefing room, the sickbay, and perhaps things like a toilet, a depository for rock samples, a holding cell, and an arms closet - things you might need soon after beaming up. Distribution of those assets, or of the transporter rooms, would complicate post-mission procedures...
Did we ever really learn what the door opposite the transporter room doors leads into? Is a mirrored transporter room ruled out?