In the 3rd edition of the Classic rules, air units were allowed to retreat. The 3rd edition also provided for sub submergence. I will need to add the stack thing.
The third edition was the CD version. The CD allowed many illegal actions (plus it did have some optional rules that you could use or not use at your discretion). The items I listed above were not permitted by the rule set that was published with the game. The programming was flawed, allowing the actions you describe to occur, and many CD players then played the game allowing the use of these flaws, incorrectly interpreting the flaws as rules revisions.
It did not make it part of the “classic” rule set.
If you want to add another subset for comparison, then by all means add “3rd edition” - enough online CD players used the rules you cite to qualify it as a separate rule set, but if you are not going to distinguish it as a separate rule set, then I would encourage your comparison chart to use the published rules for Axis and Allies 2nd edition as the point of reference for “classic”.