Almost appears as if the door Spock comes through is on the opposite side than in the set plan. Where it says "console" beside the word "forward" above the word "see" is where the door ended up being put for shooting.
He walks in, the engineering grill is on his right. The camera would be around where the word "dwg" is. The sitdown console is rotated 90 degrees, you're right about that.
If you follow the set plan, the grill would be on his left if he walked in the door that's shown - it's not accurate. I figure that when they got to shooting, it blocked better the way it ended up in the episode.
Not "almost"...that's exactly what they did. The door got swapped to the opposite corner, the second console got moved to the other end of the wall with the tanks, and the central console got rotated. Also, it looks like the room may not have ended up rectangular...look at the engle of that ceiling beam coming out near the door.
I should add that I don't think it's necessary that the phaser control room be located right behind the phaser banks...it could be directly above them on the larger deck. Adjacent doesn't necessarily mean horizontal!