This is just me, but I prefer to think the "back wall" of the transporter room was always as it was with the large, engineering MSD we see in "Dagger of the Mind". It just makes to me that it be there.
I realize that it clearly was not there in "Let That Be Your Last Battlefield".
Well, they might have upgraded the transporter room (just like they upgraded the transporter room set. Alternatively, there may be more than one transporter room.