I'm pretty surprised. I've used Calibre's inbuilt EPUB -> AZW3/MOBI converter for hundreds of books to left-align them for my Kindle. The only books where the formatting was messed up were the ones in which the EPUB wasn't formatted properly in the first place.

I'm also interested to know more about why Calibre destructively converts EPUBs instead of making a copy to work on instead. Do you have any sources for how this works?