To be honest, I really hate hand quilting over seam allowances, so I go out of my way to avoid them, either by designing quilts with lots of wide open spaces, or choosing designs that avoid the seams.
If I do have to go over the seam allowance, I sometimes stab stitch, or use a backstitch. I also try not to go nuts making those stitches match the rest of my quilting. Close enough is good enough.
Janet