I'm talking about the Write Post AJAX ability to drag meta boxes around the page for the users' convenience. Each plugin is only active on the blogs that need it, and this situation also arises when a user wants each blog to have its own Write Post appearance. (Slug under the title, slug in the sidebar, etc.)
With plugins specifically, there's a lot of this: Blog A, Blog B, Plugin X, Plugin Y. Blog A uses Plugin X, Blog B uses Plugin Y. A user moves the metabox from Plugin X to a different column on the screen. If she moves the metabox for Plugin X (on Blog A), she loses the screen options location for Plugin Y on Blog B.
I can filter get_user_option() but there is no equivalent filter for update_user_option(). Tracing back, update_metadata() is the soonest I can apply a filter to create a shadow system of per-user-per-blog preferences. I would like to know if this is an intentional behavior, a feature request, or an unintended consequence of having global screen options.