For my idea of appliqueing, the parallel 9-patch blocks would be even with the foundation block and sewn into the seams between blocks. That eliminates a tiny bit of the hand work! You could certainly center the hex units on an oversized block as well.
I don't do a lot of applique and no hand quilting at all, so no help from me there. Most of my hand quilting friends prefer cotton or wool batting and 100% cotton back.