The two songs that you called out are, IMHO, two places the movie improved on the stage production.
Regarding America America, the stage version of that song is alot different, and I strongly prefer the version from the movie. I'm actually surprised that it hasn't carried over into stage productions, but I've seen it performed live twice and both times they used the original version. Gee Officer Krupke occurs near the end of the stage production. The placement doesn't really make dramatic sense. It works better in the movie.
Of course I love those Who and Stones live albums. If you don't like bluesy Stones then of course you're never going to like Ya Ya's. I don't think you need to hear the Isle of Wight album, but I am pretty unhappy with how the butchered Tommy in the version released as a film. Was this just done to make us buy both versions? I had assumed that my taped-off-TV version was just a butchered edit of the full film, but then I found out that was the only version available.
I never really cared about The Magnificent Moodies, or whatever any given printing and track order is called, but fans should hear it.
The Secret Of Atlantis wasn't on my radar, but it's the kind of thing that interests me in that I'd watch a video or listen to a podcast about someone talking about the book, but not read the actual book.
I'm not sure I'm ever going to watch the new Beavis and Butthead. I love the show and was on board with the 2009 version, but that this point I think it's too far removed from the era those characters belonged to to be making new episodes. I know that people said the same thing 12 years ago, but rightly or wrongly that wasn't as big a deal to me at the time. The bands on their shirts are the two biggest sports-arena-soundtrack bands.