The reason there are space requirements for quilting using batting is because it is not a woven fabric and will pull apart if not secured. Flannel is a woven fabric like the minky and cotton so space between stitchings is not an issue other than for appearance sake you don't want large areas of your quilt sagging from use as the minky, flannel and cotton will behave differently from the wear and tear from use.
As far as the washing and shrinking issue goes it might not be much of an issue. The stitching will keep some of the shrinkage down if there is any and if there is some shrinkage it will give your quilt a puckered old fashioned look like you get when you use cotton batting.