I don't get how mistakes like this happen. You'd think a requirement for remastering/transferring a film would be watching the original.
Look at some of the behind the scene from TNG-HD, you almost always see an editor with both the newly scanned film and the original tapes for comparison.
Well, it hasn't been established it's a mistake at all. As I mentioned above, a couple of scenes have been radically altered, but the majority of the transfer really isn't massively different. Based on that, I would intuit deliberate intent.
I would guess a call was made to reduce some of the glowing reds which do manifest in previous video releases, and are slightly OTT IMHO.
As for the other very specific changes, who knows?