Paragraphs with spaces or with indents is personal preference. That said, I too don't like paragraph spacing. If you look at paper books, they all indent (novels, textbooks is another matter). Given that the screen size of most readers is 6", spacing reduces what you can see even more. So I too would advice to indent, it is the norm. People who like spacing should be able to do it for themselves, since nearly no published ebook does this.
For the alignment, either justify (for amazon) or don't specify it so that the reader can set it.
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