How the Kobo ereaders handles the text alignment depends on where it is and whether you are reading epubs or kepubs. The kepub reader will override all text alignment. This means that if you force ragged-right, things that had center or right will be forced to the left.
The epub reader handles it differently. It will override the text alignment set in the body tag or class, but not in the paragraph, heading and other tags. This means that unless the "normal" paragraph has the text alignment set in the tag or class, the book will probably retain the correct text alignment for the parts where the alignment is important in the formatting.
The above is the reason I wouldn't trust this to automation. I usually remove any text alignment set to justify, and leave the rest alone. But, only after examining the changes carefully.
And as you mention the margins, these are handled differently. The margin settings don't change or depend on the settings inside the books. Effectively, they are changing the page width, so whatever is set on the device is added to whatever is in the book.
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