Oh yes, I've encountered this also and it bothers me too. When I switch to Focus mode it doesn't necessarily mean that I'm not interested at all on the "plain" items. It's just that I'll read them at a later time when I have more time.
So, it could be more useful to focus the Mark-As-Read function to affect only the current view (like it does when you select Mark-As-Read inside a folder, it only affects that specific folder).
On the other hand, it could be bad practice to have Mark-Everything-As-Read not marking everything as read.