It could be so easy for Apple: Call the upgrade a upgrade and everything is dandy . (dreyfus2 pointed that out several times).
As we (not Joe Six Pack) know the retail box is a upgrade, why is Apple shy to call it exactly that.
If that is not enough: create a installer that is looking for a previous installed Mac Os or if it can't find one is asking for a original OS Disk that has been supplied by Apple with your computer.
There is no need for serial numbers and...