There's one instance in which KindleUnpack would extract an ePub that wasn't just the KF8 componenet repackaged. That would be if the file in question was to output from KindleGen and included the original source files, and those original source files were an ePub.
I've no idea if that's the case with the TOR freebies. I suspect not. With a .prc extension, perhaps they're still using the ancient Mobipocket Creator...
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