All of these answers are great, but I'm going to go a different direction and address how permutations actually can be used!
There's a branch of music theory called neo-Riemannian theory, and it looks at what we call "parsimonious voice leading." ("Parsimonious" basically means "most efficient.")
Let's say we have a C major triad that moves to an A minor triad. Here's one way:
G E (down three semitones)
E C (down four semitones)
C A (down three semitones)
Between these two root-position triads, then, we have a net movement of 10 semitones (!). Hardly parsimonious. So let's move to an A minor triad in first inversion instead!
G E (down three semitones)
E A (down seven semitones, or up five)
C C (no movement!)
This is actually equivalent in a sense; if the E moves down to A, we again have a net movement of 10 semitones. Even if the E moves up, we're looking at 8 total semitones traversed.
So here's where the permutations come into play, because if we clarify the first-inversion A minor triad as C E A, we get:
G A (up two semitones)
E E (no movement!)
C C (no movement!)
Here, only one voice is moving, and it by just two semitones!
So, TL;DR: Permutations can be used in music theory to discuss efficient voice leading, but this is a very different scenario than you were addressing in your original question. If any math fans are really interested in it, here's an article you can check out.