Hi Harvey,
I'm going by the laserdiscs, the limited edition VHS tapes that were put out in 1982 before the series was recalled by Paramount for restoration and the one single 16mm print I have, which is of Bread and Circuses. Also, most unreliably, my own memory, which noted sound differences in the 80's when the refreshed versions of the episodes came out. All of physical media I have access to seem to support my recollection. I have to haul out my projector to run the film to confirm, but when I watched it 5 years ago, I was thrilled to hear it in stunning faded mono. With no added sound effects. As I mentioned, the mono mix of Amok Time appears to be more correct.
When the Paramount and Columbia House VHS tapes and laser discs were released, I immediately noticed the missing sound of the phaser rifle impact Where No Man Has Gone Before, the lower volume of the music as we saw the dead Salt Creature in The Man Trap, the music in the main and end credits and so on. However, I never noticed any added sounds or incorrect music (City on the Edge of Forever notwithstanding). Certain episodes I had on cassette tape which I listened to repeatedly. This is why the sound mix is more important to me than the quality of the image.
The sound of the series were made "stereo" for home video release, which makes them "incorrect" as well, but they don't have as many obvious changes. While this is conjecture, I wouldn't expect them to remove two seasons worth of exterior sound effects. I would think they would have retained or added them and spread them out to take advantage of the additional speakers.
Also, for whatever it's worth, the Amazon Prime versions of the original standard definition third season episodes have, mostly, an earlier sound mix. Either the home video mix or perhaps even the original sound mix. Either way, it is closer to what I was always used to.
I hope this helps. If you or anyone else can find anything to either support or definitively prove me totally off the mark, I would welcome it. I would love to put this to bed.