You can get more problems with standing waves when you use a single subwoofer, rather than just the two main, full-range speakers. This could be why your music sounded clearer in the pure direct mode.
Of course, if you prefer the sound with the subwoofer activated, then by all means use it. My own view is that I doubt that subwoofers are used in the mixing studio in stereo music production, and even if they are, studios would surely use two, not one, for stereo separation. I sometimes wonder if it's worth using only one subwoofer for music, because of all the trouble with standing waves.