I'm not sure I understand everything that is going on here, but would this be considered forking the project? I guess that is a natural part of open source...

If the japerry d6 Ubercart is going to be significantly different in code base and concept than the ubercart.org d6 Ubercart, though, I wouldn't mind seeing it called something different. My main concern is confusion amongst users, within support forum topics, in IRC chat, and on a admin's update.php page over what exactly is going on.