With my Kobo Libra 2, if I set justification to "off", it follows the justification that's in the ebook -- which usually tend to do exactly what you're asking, e.g., justify body text while leaving headers alone.
When I switched over to Kobo a few years ago, it seemed much easier to manage custom fonts, too, although I think Kindle has improved in that regard. I don't think there's a tremendous amount of difference between the two in practice anymore, though. (In terms of text handling, that is.)
Unfortunately many ebooks don't specify a default justification on their body text, so with "off", my Kobo Sage will left-align the text in those books.
Agree that I think Kobo better manages custom fonts from what I've seen. (I don't use a custom font so I'm not 100% up-to-date on the sordid details for either platform.)
When I switched over to Kobo a few years ago, it seemed much easier to manage custom fonts, too, although I think Kindle has improved in that regard. I don't think there's a tremendous amount of difference between the two in practice anymore, though. (In terms of text handling, that is.)