The 3D audio toggle will apply the HRTF filters globally (master output) rather than only affecting world sounds.

The expected behaviour from HRTF in games is that sounds that occur in the world around the player should have HRTF applied (environmental sounds), whereas sounds that don't occur in the world (game music, ((not disc music!)), UI sounds, etc.) should not have HRTF applied. Applying HRTF filters to game music especially is a bad idea - unneeded EQ and phasing filters are applied to a source that is already in its mastered format!

I have attached a demo of this affecting game music and UI effects. The top track is with the 3D audio toggle off, the bottom track is with it toggled on. You can notice the EQ/filters affecting the quality/amplitude of the second track - something which it should NOT be doing!