Just keep in mind that if you don't do the machine applique first, before you sandwich the quilt.. unless you take it all apart --- all those stitches are going to show up on the back of the quilt..
If it were me, I would present him with ONLY the quilt top, unfinished like it is with an explanation that I will take it back and finish it for him. This way give you the leeway to make other changes and make sure it will be perfect for him when the final presentation is made.
I am sure he will love it regardless of how you present it to him, because you made it with love.
Jacke