A few things to ponder:
1. I believe a lot of flannel is 100% cotton
2. I back some of my quilts with fleece and have no problems. Some people on this board back with flannel with no problems.
3. The reason for the "recommendation" is for even shrinkage. That pretty much it.
4. Our ancestors used various types of fabrics and the quilts held up fine.... washing may be a challenge though.
and.....
5. Its your project. If you want to use flannel for any part go for it! There are no "rules" when making quilts for yourself and loved ones.