I have looked at many MOBI books in Kindle for iOS and have never experienced a problem with missing text indent or missing first lines of chapters. There is likely something wrong with your book that is leading to this behavior.
Have you checked your original EPUB for problems using EPUBCheck or a similar tool?
How are you produce the MOBI file? calibre, Kindle Previewer, or something else?
Can you post a non-copyrighted sample file that exhibits this problem?
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