I am a lifelong Dylan fan and completist.
Given the opportunity to hear competing mixes made at the time or later, nearly every time I feel the best choice of mix was made for the original release. This applies for other artists than BD. This may be because the team was hot in the original sessions. It may be that I have become so accustomed to the mixes released at the beginning that I subjectively feel anything else is wrong.
Where a new mix is made many years after the first sessions, the original artist is not involved in their creation. So BD almost certainly approved the new mixes but equally certainly was not involved in making them.
I feel there is a tendency to create new mixes just for the sake of it, or even as a gimmick. This would apply to the Beatles remixes issued some years ago when John, George and George Martin were not involved at all.
Specifically on the TOOM mixes I find most of these inferior to the originals. Many are musically less complex and for me tonally less engaging.
It is reported there were more than 30 studio takes of Like A Rolling Stone. The band and producers had pretty much given up before the released take was recorded. It is said Dylan was ready to abandon the song, as he abandoned some other great works in the years after 1966. The released take is acknowledged as one of the greatest tracks ever recorded. It has never been re-mixed.