I couldnt; get calibre to convert to PDF without indentation - having tried all the things in these threads. Then I discovered that the .CSS file being included in all my HTML files had paragraph indentation set. I removed that and solved the problem.
So, search for text-indent in all your .CSS and .HTM files and make sure you aren't setting it yourself. (I had "borrowed" some typical EPUB .css files from somewhere)
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