My trouble if I don't pre-wash flannel is the seam allowances. If you don't have at least that 1/4" seam allowance on every seam--and I mean every seam--some of the thinner flannels will pull loose from the seams.
Not all flannels shrink the same. The good heavy quilter's flannels don't shrink much but the Joann's snuggle and sew-comfy or whatever they call it shrinks a lot so if you combine them in a quilt without pre-washing first--you're asking for trouble.
Starching or sizing flannel & pressing with a good hot iron before you cut will help tremendously and the good hot iron is shrinking it for you. I have had flannel quilts come apart at the seams because I didn't prewash or starch it well. Better safe than sorry!