I'm not sure who came up with the idea of these 'flanges', but they obviously didn't have the final quilting process in mind
. If you don't quilt over them, I think they look 'messy' unless you SID right alongside. If you DO quilt over them, they can also look messy if the quilting isn't dense enough to hold the edges down - it looks like you forgot to stitch a seam. And as someone said, you have to be careful not to catch the flange and flip it.
If you are going to stitch over it with the pattern anyway, you may want to just topstitch it down, then it's both out of the way and all secured down so it won't look lumpy and bumpy.
Andi