Using a special place instead of a bookmark is a design decision.
Bookmarks are user datas and package should not modify the user
configuration. I'm marking the bug rejected, that's nor really a bug. If
you want to discuss that change feel free to join the ubuntu-desktop IRC
channel or mailing list
** Changed in: nautilus (Ubuntu)
Status: Needs Info => Rejected
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"Documents" folder bookmark double entry
https://launchpad.net/bugs/62525
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