MST3K has to clear copyrights for the original films, even though they "mark up" those originals in the same way that McMH does. RiffTrax did not have to clear rights with anyone, at the cost of some customer convenience.
I don't know for certain whether MST3K licensed things because they had to, or because they didn't want to be sued to Hell by film catalog rights-holders. It certainly seems like ridicule, commentary, and parody to me. I don't think it matters all that much whether anyone makes money from it or not. A professor can fairly use photos for educational purposes in a class where all the students pay tuition, right?
As a potential juror, I am prejudicially biased that McMH's use is fair use. If I were a judge looking for a test, I think I would ask "Is it sufficiently transformative that this use does not compete with the original?" For MST3K, you're making motion picture entertainment from existing motion pictures. Watching the MST3K version of a work competes with watching the original. So MST3K is not fair use. But reading McMH does not compete with browsing those real estate listings. So it's probably fair use.