Take into account how URE works with meta boxes. Meta box exists only at the page for which it was created. Post meta boxes exists only at the post editor page, etc. So URE remembers active meta boxes when user opens pages. So to see meta boxes list at the URE “Meta boxes” dialog you have to “show” those meta boxes to URE.
When user deactivates plugin, which have created meta boxes, those meta boxes are still shown at the URE’s list. That’s why a ‘X’ icon to the right of every meta box row is presented – to remove from URE’s list a meta box, which does not exist at WordPress anymore. It works globally for all roles at once.
1) URE does not restrict administrator role in any manner. All URE add-ons follows this rule – administrator as superuser can do and see all.
If you need power user with less permissions than superuser, create a copy of administrator role and restrict it.
2) If you suddenly delete some meta box from URE list, it’s easy to return it back – just open the page where this meta box is shown. URE will remember this meta box again.
3) Possible has sense. But user will have to “teach” URE again after that – open pages with meta boxes, in order URE can catch and remember them.
