I think the reasoning behind cutting is so the quilt doesn't get too heavy. It could also be quilters of the past were frugal and trying to save every last scrap. I haven't done any truly large appliques. The only cuts I've made in back of the ones I've done was so I could stuff them for additional effect. I stitched up the cuts afterward. I wouldn't call it trapunto. My work is a little crude for that.
I've also seen arguments against cutting away the back fabric due to it can weaken the quilt. I don't know how much difference it makes but I tend not to trim out the backs.
Rodney