1) Its not a cover image copied twice its a thumbnail, which all PRC based formats include, because they were originally designed for Palm PDAs that were too weak too dynamically generate their own thumbnails. Compare the file sizes of the two seemingly identical images.
2) There is no guide in an AZW3, the guide you see is a reconstruction the editor creates for you, dont worry about the multiple entries.
3) Again completely harmless. This is a peculiarity of the azw3 format. I need to get around to muting that warning when running check book on azw3
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