I've realized what I can compare the TMS controversy to: the Live Aid controversy. When Live Aid was released on DVD there a while back, some footage had been lost; some was of such poor quality that it was unreleasable even if restoration was done; some footage suffered from problems on the day of taping (a generator infamously exploded during the Who's performance). So, all the missing or "bad" footage was left out of the set. However, there were about ten hours of existing performances, plus bonus features, plus a 45-minute documentary that was on the set. Fans of Live Aid were outraged, saying that the entire concert should have been released. The reason all of that was left out was because it couldn't be included.
The same thing is going on with this set. The five songs are out of the set because the rights are so prohibitive that they just can't be released. The same thing happened with the Ed Sullivan disc a few years back.
Now look: Muppet fans have been waiting for season sets of TMS since the first DVD was released. Now, don't let the omission of five songs (probably totalling up to about twenty-five minutes of footage) ruin the experience of seeing the first season of TMS in beautiful picture quality and wonderful sound, with great bonus features and packaging for you. It just shouldn't happen. Buy the set, and revel in what is there. Don't focus on what has been left out.