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Actually, computers should stop assuming that "extension is everything". TIFFs and AVIs are containers with a single extension and lots of possible content, knowledgeable software knows (or should know) how to manage this, I don't see why it should be different with ePUB.
I agree it is going to be a problem for users if the same "name" is used for different incompatible DRMed formats, but it shouldn't be a problem for the software.
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