I agree with most of the things in the OP, but there are a few points I would like to elaborate upon:

-I think Super Sonic should be allowed. Free DLC is basically a non-forced update of the game, and using the latest version is perfectly reasonable.

-I also think Wispon switching should be allowed, because it seems ridiculous to disallow intended features. Perhaps a clause could be added to add X seconds for each switch used, or to have time spent on the Avatar screen be counted as run time.

-There's a contradiction between the arguments that NG+ All Stages is tedious and that NG+ doesn't have to worry about losing RTA to missions. If someone has time to get all the S-Ranks and Use X Wispon/Y action to defeat Z enemies and three Gold Medals on their Avatars of choice in order to avoid potential mission pop-ups, they have plenty of opportunity to get all the Red Rings. I do agree that a leaderboard should be dependent on whether or not people actually run it since they haven't so far, but we shouldn't dismiss the idea out-of-hand.