I think that the main reasons Michael would remove songs from the set (I'm assuming, don't take my word for it) would be that he was tired, and didn't want to risk damaging his voice more, or not being able to keep performing at that level. Many forget that Michael turned 34 in 1992, already in his mid 30's doing arguably the most intense tour is demanding (again, just assuming).
One thing I think people forget is that, even though his microphone was off, he was still singing; we just couldn't hear it. Take for example the snippet from Munich 97 'in BOTDF where he hear his live vocals, he was singing, but he sounds hella fatigued. Michael I'd say hit his peak performance ability as an adult in 1988/89, don't get me wrong he was still always performing at that level going forward, but he paced himself. In 1993, you can notice that the beginning of Jam feels less "hype" than the 92 'leg, because, he was 35 years old, he can't use up all of his energy immediately. He does a lot less of full dancing throughout the song (save for the dance break) than compared to the 92 'leg. He began picking and choosing. Scream for example, you notice that his particularly difficult moves are spaced out in that song. You make a good point that he does a lot more walking than dancing sometimes in his songs like Scream, Billie Jean. Thats my theory on that.
Another thing worth considering is pacing. Maybe the pacing wasn't to his liking. IDK, haha Basically my main points are: He got older and couldn't keep up the same energy for 2 1/2 hours, and the pacing. Again, thats just my theory haha.