1) Both are similar but you should note that kindlegen is the only official tool that guarantee minimum problems. Calibre mobi output is a result of reverse engineering since Mobi is completely closed format. You should also note that calibre during conversion dramatically alters original book code.
2) Yes. It's true. KF8==AZW3. AZW3 are still likely be rejected by Amazon cloud.
3) I don't know. Maybe you should ask Kovid Goyal - calibre author.
4) Yes. ExtractCoverThumbs restores to your Kindle missing cover thumbnails for AZW3 (converted from dual Mobi by Amazon cloud servers) books downloaded from Amazon cloud.
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