1) Yes.
2) I've never annotated, but highlights are stored in a myclippings.txt file and are complete (though unformatted, since it's text, and I believe there's a limit to the size of the clippings)
3) Yes. More importantly, the Kindle defaults to justified text, and unless the book is designed with the "text-align:left" style tag, then they will always be justified.
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