It would help if the pieced seam in the backing is ironed open.
I wouldn't worry about shrinkage. If the machine quilting is moderately close, shrinkage becomes controlled by the batting. In other words, if quilted adequately, the flannel will not shrink significantly more than the batting. I once took a class from Harriet Hargrave and she brought an all-flannel quilt of her own that she made to prove this. She did not prewash the flannel, machine quilted, bound the quilt, measured it, washed it, measured it again and it was fine. I was able to handle the quilt and look at it closely, so I am sure about this. When flannel fabric is washed on its own it will shrink many inches; however, after it is quilted to a batting, the batting prevents it from shrinking as much as it might otherwise.