It's not necessarily bad to use unwashed cottons with poly batting. Often you will get a little of the antique crinkling effect from fabric shrinkage. Personally, I prefer the antique look so that would be no problem for me.
Flannel, however, is in a category all of its own. I would recommend pre-washing and drying the flannel at least once before using it as a backing. While it might not be an unmitigated disaster, it could end badly if you don't preshrink the flannel. This is because some flannel shrinks *drastically* when washed and dried. It might be okay, because the quilting stitches prevent the flannel from shrinking to some extent, but I wouldn't want to take the chance.