I think your project would work. You are in essence making a "comforter" inside your cover. The only thing different from a duvet cover would be that you are sewing it to your middle "comforter". Hmm - pretty ingenious, I must say. I, like you, find that duvet covers are a bit of a pain in getting it to fit and then putting it back on when it is washed (ok a lot of a pain).
Come back and let us know how it worked out. This sounds great!