What is your source for this information? I mean, we've speculated and I've even thought that you might be right, that there will be some sort of check, but do we have any definitive information from Apple?
Also, I suggested that for OS X, Upgrade Version = Full Version. There is no distinction with Mac OS X as there is with Windows. IE: No retail box of Leopard (Tiger, Panther, Jaguar) said "Upgrade" on it. This Snow Leopard model is really a first for Apple with OS X (10.1 was free, but that's a different story).
The question that I sort of posed in my second paragraph was, "What are the technical differences, if any, between the retail disk and the box set disk?" Fundamentally, I'd agree with you, a $29 retail copy is an upgrade for Leopard users, while the copy that comes with a box set should be the upgrade for Tiger Users.