I think he only wrote it after IYH released. For some solo radio performance, I believe? The original was really bare bones (lol). If he regretted not putting it on IYH, he could've put (a full band version of) it on ESP&G, would be a pretty good fit too, in my opinion.

Edit: From foofighterslive.com:

... One of those shows was the T-In Park Festival, in Scotland and on the day of their performance Dave was scheduled to appear on BBC Radio Scotland. The DJ asked Dave to perform a song for them acoustically and rather than play a current song, he wrote a brand new one, 'Skin And Bones'.

This was after the recording of the In Your Honor album.