I have seen a method where you stitch your trapunto design through your fabric and a layer of batting, and then you carefully cut away the excess batting from the underside, as close to the stitching as possible. Repeat for all areas you want to be "trapuntoed". Then you proceed the same way you would with a regular pieced or appliqued top- top, batting, backing, quilt together and there you go!
Seems like it would be much faster and easier than the traditional method, but I understand that some things, like thin stems, don't work as well with this method and that couching piping or going with the traditional method is best for those kinds of things.