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If you sideload something into your nook app on your iPhone, it won't even appear on your nook unless you separately load it into your nook as well. Tracking of recent purchases/opens and last page read is done through the B&N servers. The B&N servers don't know about your "My Files" or "My Documents", only your devices do.
If I'm wrong, I'll be happy enough that all my Baen books will sync...but I doubt I am wrong. Whatever is being sync'ed needs to be in the cloud for the tech they are using, and what Amazon does is allow you to upload stuff into their cloud (as I understand it).
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