Wellll....just to be clear, would fight music from "The Omega Glory" (when Kirk unties himself in the room) which seems to be a rearranged version of the Kirk v. Mitchell track from "Where No Man Has Gone Before," find its way on the box set?
I don't recall any re-recordings of pilot music in the second season. However, IIRC, Fred Steiner's "Mirror, Mirror" score did feature a new arrangement/variation of the Kirk/Mitchell fight music, and that cue was used several times throughout season 2, so that may be what you're referring to. So it would probably be included in the "Mirror, Mirror" score.
For that matter, i'm guessing the WNMHGB fight music is included?
I recall that was not a part of GNP's TOS pilot album...huge disappointment back in the day.
The last few minutes of the WNM score were left off that album for reasons of length, because LPs could hold less than 2/3 as much music as a CD. I don't think any of the episode scores originally released on LP were unabridged, except maybe for "The Cage." But this set is 15 CDs, roomy enough that they can include extra bits like library tracks and alternates, so it's safe to say that nothing from the actual episode scores will be left out for lack of room.