If you are talking about making a level pack as one WADfile, then compiling music for it in a different WADfile, the answer is yes as long as both files are in the same release. (as far as I know)
People do this often to make their modification netgame hostable (downloading a 22 MB music WAD isn't hostable) version of the mod that doesn't include the music, and then have the music available so you can add it for single player.