I'm not techincal so can't help with the XYZ muscles thing (am sure there are some physios on here who could explain) but I think the reason we ache when we're not tunnel fit is that we're continually having to push down onto the air which is being pushed up at us to fly our bodies and make changes in position which is different from skydiving in that in freefall we're using gravity. Of course muscles are required in skydiving too but not to the same extent.
I can tell that I've left it too long between tunnel trips by how much I ache the day after and the day after that which is worse due to DOMS (delayed onset muscle soreness).
As Chris says, the happy solution, not that you asked for one, is more tunnel more regularly! Yay!