The difference is more than just the cowl. The Super Cub is wider at the nose, opened up cabin top, has flaps, and the DA-100 won't fit inside the cowl on either one. I'm building the Super Cub and powering it with a ZDZ-80. Should be plenty power for areotow and float flying.
Here is a link to another Super Cub thread you might like to read.
http://www.rcgroups.com/forums/showthread.php?t=481234