Yes. Do what you think the quilt requires.
I just got in a beautiful quilt from a customer and it is appliqued and has a million glass beads on it. I won't be able to get my longarm foot anywhere near the beaded appliques or those beads will break all over. So I am machine quilting her borderes and her sashing, and hand quilting the appliques. It's what the quilt requires.
Ya gotta do what ya gotta do.