Lack of control of what? You understand that with Y axis enabled any pitch rotation changes the point of view elevation regardless of any "precise control" right?
Oh and what bad habits?
Pitch rotation only grossly affects elevation at the limits of range of motion. Parallax 101.
The bad habits are not learning to control your head movements. Instead of learning to control your head movements, you're adopting sloppy control and using the software to cover up the deficiency. It's similar to removing your cars ability to turn left because you have problems executing left-hand turns. You could probably compensate quite easily without the ability, but in the end you're covering up a deficiency by not addressing the underlying issue.
I use TrackIR and I'm speaking from first hand experience.the ability to change elevation is very helpful, and therefore you're somewhat limited without it. It's the same idea behind stick scaling and why I recommend (and fly with) scaling off on all axes.
Notice that even with up and down movement, my head returns to center:
http://youtube.com/watch?v=VC_xhithN4w&t=55It just takes practice. That said, do what works for you.