I would still leave a little wiggle room on the background fabric to square things up. For fused applique--you cut the pieces to finished size and then use a blanket, zig-zag or satin stitch to hold them down. I've even seen a topstitch used but that is rare. Sometimes the fabric gets a little skewed during the process of sewing the applique down so that's the reason I allow for extra background fabric on any type of applique.