Hi Keith - just for your reference, I see what you are trying to achieve (and I have done similar with other plugins in the past, but not this specific one).
Obviously it would be impossible to setup controls for all the plugins out there (and keep them updated). Also, there are so many variables to this - it really does depend on how the author has coded thir plugin as to how much you can interact with their code.
You have got me thinking though, I can see a need for this for users (and myself), but it's just how to do it. You start adding custom user controls, and you need individual role control for each - what if they had 8 different controls from plugins?
I have just rolled out v2.5 update, which brings it in-line with WordPress 3.1 (including custom post thumbnail control...finally!). I do have some other ideas that I'd like to bring to the plugin, but a solution for plugin meta boxes is now on the list. Don't hold your breath, the first implementation will more than likely allow you to define your own meta box manes, but be a blanket 'one setting for all' on the boxes inserted by plugins. This should suit most users requirements though.