I am not sure what you have been reading, but I have never had trouble with flannel. Or maybe I am just not as particular as some others??
I am currently working a quilt that will have a completely flannel top and will have a cotton backing. I have a 5" outer border, but no inner border.
I did not prewash any of the fabric - but I purchased quality fabric. I think some fabric is not as high of quality as others???
I sure am not of much help for you, I have never seen the problems that you are talking about.
I sure am going to pay attention to this quilt that I am working on now
Will be interesting to see how things end up as I watch for those things that you have pointed out