I have a different view. I’d quilt the background/backing/batting and then applique over the top and quilt as you need to for the appliques.
I made a baby quilt once with an elaborate design of overlapping circles and did it this way. The circles were topstitched down and quilted in spaced concentric circles. The background quilting didn’t show through and the quilt itself has held up very well. Did 2 of them, actually, with the entire quilt quilted before applique.
With a wall hanging, it’s unlikely to be washed, so durability would be a slam dunk.