Mike Nelson, Kevin Murphy, and Bill Corbett make a living out of mocking just about anything in sight. I never took their ribbing on Shemp all that seriously because often their jabs at such things are very tongue in cheek. In their RiffTrax for the film Daredevil, the trio pretty much tear Kevin Smith a new one in his cameo in the film, yet in an interview afterward, Kevin Murphy claimed it was nothing personal, just mocking him for a laugh. Murphy also claimed Smith's Dogma was one of his all-time favorite films. And Kevin Smith himself is an outed fan of Nelson, Murphy, and Corbett's previous television series Mystery Science Theater 3000.
However, using them as bumpers for Legend's Three Stooges DVD was a little out of place. But Mike Nelson was under contract to Legend Films to use his cult status to boost sales of their colorized line by recording mocking commentaries for the films they released, so it's understandable why they used them.