I think that another example of Metallica doing "whatever" with the timing is just in the previous song in the album, Battery. If you try to follow the beat, it mostly follows a 4/4 but sometimes they just cut it short. I feel it's more accentuated in Battery, because it's a little bit more random and contributes to the rushed feeling of the song.
Assuming you're talking about the "chorus" where the lyrics are "Battery --- Ba-ter-ry!":
"Battery" is certainly not the same type of "whatever" as "Master of Puppets". It's also not cut short. They're adding in an extra beat (a quarter note), resulting in one measure of 5/4 (or an extra measure of 1/4, but the notation makes more sense in 5/4). I think it's clear that this was intentionally and explicitly composed with an extra beat (Metallica adds or removes quarter notes in riffs fairly often).
"Master of Puppets" on the other hand was very likely not intentionally composed in 21/32, but I think it was intentionally composed with the "microtiming" in mind as a feeling.
A lot of people in this thread seem to think it may have just been Lars's fault as a crappy drummer. But James was notoriously meticulous with the tightness of that album as a whole (and AJFA). This is not sloppiness and it's not 21/32. It was intentionally composed by feel or by informal directing ("let's do that part by skipping a little, like ba-DUM-DUM, you know?").
Not really the chorus, but mostly the instrumental part at the beginning (after the, let's say, acoustic-slow part). I think there's some short timings there too.
Likewise with a lot of System of a Down's music; most of it sounds like a straight 4/4 but it often feels quite clipped at the end of a measure. Their song Question [0] is a great example of this feel, it's like one-a-two-a-threefour.
