I can understand your concerns. And the header things sounds like a problem. I meant the white space in justified text is not solvable. As to the format: I am not a kindle expert, but as far as I know, old readers use mobi, moder kf8. And amazon takes care of sending the right file to the user. If you use kindlegen to convert your epub, the file (with a mobi extension) includes both versions.
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