1. 3MCs: Not sure on the Skinny Boys sample. My best guess would be artistic choice.
2. In Sound From Way Out: This was originally a vinyl only mail-order release that was a compilation of tracks from other Beastie Boys records. You sent your check to Grand Royal and they shipped the record and I believe that was the only way to get it. Sometime later they decided to do a wider release, and at that point they went back and made alterations to certain songs, like removing lyrics from Lighten Up and Namaste. It's a fairly safe assumption that they had a small-scale project that caught on and when the did the wider release they decided to put some more effort into the audio program.
3. Time for Living: Here's a description of what's going on.
https://www.sweetwater.com/insync/out-of-phase/. Was this a thing with Mullet Head too? Anyway, I can't remember if this was an intentional choice or not. Seems like something MCA might have done on purpose.
I'll have to check my Pass the Mic etched record. I wonder if that's a pressing flaw.
4. Beastie Boys Music. This is almost certainly just a pressing plant error. You hear about this on occasion with other records.