I remember having a discussion with Shane Johnson about 11 years ago about the phaser emmitters as he had done a small set of exterior plans that came with a decal sheet designed for the 18" kit. As I recall, his plans said the ring just above the sensor dome was a phaser turret, which was designed to swivel around. When I asked him about it, he said based on his research that Matt Jefferies himself came up with the turret idea. The model didn't need to show swiveling, but that is where phasers were fired from for the most part (depending on who did the optical compositing).
The bumps on the saucer for phaser banks as I recall was something Franz Joseph came up with. Of course, Joseph did mount photon banks in the B-C teardrop topside, which was contrary to what the episodes showed when Photons were fired. But it appears that Franz's phaser bank bump idea found their way onto the TMP refit saucer.
The photons are a bit of a weird animal. It looks as though Trek didn't seem to introduce photon torpedoes as weaponry until mid-way through season 1 and never really fleshed out exactly what they were fully. But to represent them, they used the weird blanket phaser fire/depth charge animation that was created for "Balance of Terror," probably because it was so different from the phasers used in the previous episode where they were seen, which was "Corbomite Manuever". Eventually though, as the episodes progressed the photon torpedoes were fleshed out more. Somebody I suppose could argue that the "nipple" on the sensor dome is indeed the photon launcher as MR seems to have done, since it was never present on the Pilot 1 or Pilot 2 versions of the ship. It seems like as good an explaination as any.
For the Phase 2 ship, the area in the neck pylon that became the photon launcher on the TMP refit was originally intended to be the main phaser bank. The story bible for Phase 2 (excerpts of which are printed in the Phase 2 trade paperback written by the Reeves Stevens authors) mentioned it. The reasoning for putting it there was it could draw more power from the ship's warp engines. That concept of course became a plot point in TMP (and we never saw them fire as the anti-matter imbalance cut them off when the ship was caught in a wormhole). Funny enough, an error in the TNG episode "Darmok" had the phasers firing from the photon launcher on the D. So what was originally supposed to be a phaser bank on the unfilmed Phase 2 E which became a photon launcher by the movies, for one episode became a phaser emmitter again.
Now the one thing that has kind of jacked up phaser and photon launchers on the TOS ship though is what the Defiant used in the Enterprise episode "In a Mirror Darkly". There we had phasers and photons coming from not only the front lower dome, but also the aft secondary hull dome (which previous plan sets interpreted to be a control tower for the shuttle bay). But when you think about it, having a phaser and photon launcher on that dome makes logical sense as if the front dome acts as a turret, it can't fire due aft anyway.