@ach As far as I understood this bug report is about the problem that the page tools are moved down to a position that is no longer on the screen when you are using ?do=check or rather when a lot of notifications are displayed. What my screenshot illustrates is that this also happens when there is just one notification and your screen height is a lot smaller, i.e. that a special fix for ?do=check won't solve the problem. You are right that a full fix for this phone in landscape orientation isn't really the topic of this bug report.
The problem here is that the page tools are relative to the div with the class "wrapper" which contains the content and the sidebar. This div is moved down when messages are displayed (they are in the "header" div). I can't think of a CSS-only solution that won't introduce new problems (like that the message become part of the page content or the page tools stick to the header) but this could be solved in JS with something like http://stickyjs.com/
(with some more code in order to not to modify the current behavior if everything fits).