While piecing together batting can be done with no evidence of it in the completed quilt, I doubt that can be done with flannel without some feeling of the seam no matter how you do it. Batting has loft to completely hide the seaming once in a quilt as traditionally when batting is pieced together it is butted end to end with no overlap and basted together or using a large zig zag stitch. Any bulk created by doing this is hidden in the batting's loft and further camouflaged by quilting.
As flannel has no loft to it there is nothing there to absorb the extra bulk produced by a seam. I would think with flannel as your batting you would definitely feel the lumps made by seams in quilts you have already done this way. Especially where there is a lot of bulk coming together like in a pinwheel block. If you want to go ahead and try, I would recommend a larger seam allowance, perhaps the standard 5/8" used in clothing assembly and then press all seams open. This helps make the bulk of the seams less obvious. But I am fairly confident you will feel the lumps of multiple seams if the seamed flannel is used as batting. Especially many small pieces all pieced together. If you will only have like 4 seams in the whole thing then it probably won't be noticed any more than the seam bulk you already have in a pieced top.
Edited to add, I would love to see a closeup picture of any of your flannel batted quilts. I am curious as to how the quilting shows on one of these and how they hold up to washing and don't become totally wrinkled.
Last edited by feline fanatic; 09-03-2019 at 10:31 AM.