I have made some side-by-side comparison between the US and Japanese LDs starting with the episode which has the most obvious audio changes, City on the Edge of Forever. I did encode both LDs with the exact same settings from my Pioneer player. Here’s a sample :

Picturewise, this is exactly the same transfer. Colors on the japanese release are a bit warmer, but this is the very same transfer. The exact same defects can be seen on both :

Surprisingly, the original “Goodnight Sweetheart” music has been kept on the Japanese LD, on both english and japanese tracks (even if the sleeve says the opposite).

There are some forced japanese subtitles here and there for scenes that haven’t been dubbed in Japan back in the 70s.

The Opening sequence looks like crap on the japanese LD and is from the second season. The original first season opening is on the bonus LD from the jap boxset.

The trailers are included AFTER each episode ending. Desilu/Paramount logos are not the same than on the US release. City on the edge have the Paramount zooming logo from 1968 whereas the US LD has the blue montain Paramount logo from the 70s.

The audio is of course much better on the japanese LD since its digital mono and can be transferred losslessly to a PC. The Japanese LDs also have chapters.

So yes, I would start from those japanese LDs, these are the only TOS release with the original digital mono sound.