The point deduction rule has always been in effect it's been used from the begining.
This same situation happened with Lopez-Alvarez, Lloyd-Vaca and as you stated JCC-Randall.

It's not the fairest of rules but it wasn't just made up out of the blue.

About the doctor asking JCC. If you watch Arce-Hussein, JMM-Jaca or any other bout with a head butt the doctor more times then often will ask a serious of questions raging from how he feels to if he can see or if his head hurts, can he continue..... The questions he asked IMO were not out of line and or something that's ilegal. Ultimately the doctor has the final saying. I think the doctor should have told Mills he's OK to continue THEN once JCC turned to Mills and would say something like 'I can't go on' or whatever then Mills would have had to call the fight off on retirement by JCC. Thus making Randall the winner. I do think that situation was not handled accordingly.

A similar situtation BUT really blatant and full on robbery can be seen in Armando Muniz vs. Jose Napoles I, when Napoles suffers a cut and the fight is stopped by the doctor. They go to the scorecards and Sulaiman, the judges and the ref. get together and huddle up and award the victory to Napoles.

About the 3rd fight how can you say he was a name trial horse. Randall went on to have one of the best trilogies with Coggi. Have you ever seen the fights? Randall went on to become the WBA Champ.
His career went on the decline when he was upset by Khali.

You can't blame JCC for rematching Taylor I mean he fought Randall twice back to back, and needed to get back in with Taylor after the way their fight ended.