Comment 9 for bug 858957

I am not sure why you think there is a problem here, calibre by default
stores an extra copy of the bookmark data inside the ebook file if the
ebook format supports that, and there is an option to disable that if
you value unmodified files more than you value being able to store your
reading location and bookmarks together with the ebook.

Since you apparently feel so strongly about this that you revived a
6-year-old bug just to tell us the design is somehow wrong, I can only
assume you know of a better design.

Please tell what the better design is, other than simply removing this
*optional* feature.