There's no reason that comparing two would be enough... could be some things common to any two different copies but not any others.

Back when versions were being leaked and people tried to patch out their IDs Pierre would quote that 98% of the watermarks were left or so. Ilfak's not stupid, I'm sure he's come up with something quite crafty and not easily resolveable to an unidentifiable but still functional version.

Disclaimer: Haven't looked at it in any detail. I'm a big IDA fan and paid up user so I don't want to hurt them ;-)