Eh a little hacking never hurt anyone. This theoretical method I suggested doesn't even work at the moment anyways. I bought an Amazon book, and had a PD book of the same title and only the Amazon book successfully synced with the server. I'm sure its more complicated than just title/author anyways though. The way I see it, Amazon can either add functionality or I'll find ways to add functionality for them.
Moral of the story is, Amazon needs to stop being so closed and open up a little. This lack of syncing for all books between the two devices is the only thing really keeping me from ordering a Kindle this very moment.