Properly formatted commercial books should not need this step. Properly made user-generated books, ditto -- probably more on mobileread are good to go.
Calibre is not an editing platform; it's for conversions. So, yes, it's helpful when you are creating your own books in Word -- but this isn't a step anyone should have to do (and that's a source thing, not a Kobo thing).
Are you asking for multiple bookmarks in the same book? I am having no trouble with one bookmark per book (simultaneous bookmarks on the device but one per book).
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