MaryKatherine--have you talked with your client about your concerns? I'm wondering if she did not pre-wash the top, having her pre-wash the back won't make any difference in the long run. So guess I'd go ahead and quilt and tell her to expect it to do lots of crinkling when she washes due to nature of flannel, maybe suggest that when she does wash, that she lays flat to dry since air drying won't shrink as much as dryer heat.
As far as quilting--i'm thinking that a less dense quilting will cause less stretching as you quilt. I'd be most concerned about the back stetching and getting puckers. Maybe before you put the bat and top on the frame, you could spray the back with water to get some shrinkage and avoid the puckers??