We don't use the default XF one (if you haven't noticed). Either way, at the end of the day it serves very little useful purpose, and I'm be more inclined to do away with it than move it up top where it interferes with links and navigation (if those were my only two options).
I don't understand why it would interfere with links. People are waiting for something to happen, why would they want to click a link...? Or did you mean something else?
It definitely happened... was the whole reason it was removed from the top because it was causing issues. For example, there are some things that are done via AJAX that aren't triggered by the user.