You also forget that CSS is also supported in some of the ebook formats, which adds extra control to the creator, while still keeping it flexible. Also HTML by itself is more than just basic left, center and right justification. It can do more, if you know what to do with it.
Also, the ePub3 standard also supports HTML5, which can do a lot of incredible things. I've even seen epubs using HTML5 that had video built in, not to mention vector graphics.
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