Well, their definitely not coming from the lower dome. But the ringed area seems like a good option to me, especially seeing as how that are would sort of correspond to the refit, as Timo
may be suggesting above?
Even though the original footage from "Arena" seems to be suggesting the beams originate higher, up, if I were to play the "producer's intent" card, I would have to assume that that is a simple error in the printing of the optical effect and they had every intention of having those beams come from the area of the dome, as per usual, but they just "missed," probably by either goofing up the cel animation or else not having the equipment lined up right when they did the superimpose.
But, in a WWTTD world, that is
where those beams are coming from. I have no problem with assuming there are in fact a ring of phaser emitters at the level of the emitters on the TMP refit ship. Possibly these are the mid-ship phasers and the main phasers are located just forward of the lower sensor dome?
I only have the the 1st season of TOS-r on DVD and I'm too stubborn to subscribe to Netflix so I have no way to actually watch this scene in motion...