I don't clean up my seams like you do. I trim the ends of my stitching line, the thread not the fabric. When it's all pieced together I trim anything that is hanging loose (fabric frays) if they are overly noticeable. These seams will all be trapped between your top and the batting and quilting will hold everything. I would worry with what you do that you would be losing your quarter inch seams. I think I would have to see how much fray you are referring to in order to see if it's necessary.