Fray Stop dries fairly hard. Not sure I would want to use it on a quilt, even in spray form. Fray Block dries softer but, again, I have never needed to use this on a quilt.
How wide are your seam allowances with the flannel? It's a good idea to use 1/2-inch seam allowances because of the tendency of flannel to fray.
However, it looks to me as if this is only the quilt top. If you are planning to actually quilt this top (rather than tie), then the quilting should hold the quilt together sufficiently that the frayed seam allowances never actually come apart. It helps to use a fairly close all-over pattern if machine quilting, or quilting on each side of each seam allowance if hand quilting. Those types of quilting will prevent too much stress being put on the seam allowances.
If you still really want to stabilize those seam allowances before layering, then I would recommend using MistyFuse. Some people use MistyFuse routinely on the backs of their quilt tops to stabilize them before layering.