I do machine applique with freezer paper, but use the following instead of freezer paper when I don't want to remove the backing fabric:
https://www.amazon.com/gp/product/15...?ie=UTF8&psc=1
This is thicker than freezer paper, making the applique just slightly puffy, but basically the bonding that holds the fibers together disintegrates in the wash so you have just a few extra fibers within the applique. I like it better than the other wash-away applique foundations I have tried because it is easier to get a crisp edge with glue. I found Sharon Schamber's wash-away applique foundations too soft, as are all the other brands I have tried. It also has the added benefit of being fusible on one side. I could never use the Appliquick tools; I am way too clumsy!
It is pricey but, at my age, ease of use takes priority over cost. I do not bother to use it in large appliques, however. Mostly I use it to save time on smaller appliques. With large appliques, I have never found fraying to be an issue even with the backing cut away, as the edges are still encased in batting and backing. Assuming the quilting is reasonably close together (say, 4" apart or closer), there really is not a high probability of fraying. My guess is that there is a higher probability that your hand applique stitches would come apart from the agitation in the laundry.
Edit: I should add that on large applique shapes, when I cut the backing away, I typically leave as large a seam as possible -- usually 1/2" minimum. This provides insurance against fraying.