Unfortunately, Kindle for iPad is a huge mess.
I experience the same problems you mentioned (problems with padding, margin, and text-indent), and I reached the following conclusion: for my mental sanity, I give up trying to have the text look ok on Kindle for iPad, as long as it looks fine on the "real" Kindle's.
(My suspect is that they do not want to have a "full-fledge" Kindle app on iOS, for "obvious" (many quotes here) commercial reasons.)
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