I've been known to turn to self harm every now and then. I mostly use it because physical pain is what (in my mind) I feel I deserve; other times I use it in order to get out of a dissociative/hypervigilant state. If you didn't feel anything helpful, you might not turn to it again.

"...how fatigue and chronic illness -- mental or otherwise debilitates you to a point where "rational understanding" becomes irrational."

This is very common and if it bothers you, definitely bring it up again with your therapist. Don't let him skate over it; make him understand how much of a concern this is for you. If it's a concern for you, it should be for him.