I have used Sue and Pat's raw-edge technique on several pieces., mostly small things like wallhangings. If you are going to mix threads for the blanket stitch, be aware that the weight of the thread will determine how visible the stitching is. It probably would not be ideal to mix 50 weight with 40 weight, since the heavier thread may produce a more prominent edge, making some patches stand out more than others. It certainly would be fine to do all the appliqué with the heavier thread, if that is the look that pleases you. The other thing to be aware of is the sheen of the thread. Again, you may not want to mix a matte finish thread (such as cotton) with a shiny thread (rayon or some polyester) if you would prefer a fairly uniform appearance to your appliqué.
Having said all that, I will freely admit to grabbing whatever Coats and Clark's Dual Duty thread is handy and the right color for my previous projects! For the BOM, since I consider this an heirloom piece, I will probably stick with 50 wt cotton Aurifil or Mettler. But as Margo says, it's YOUR quilt, so do what pleases you!