But surely not from the real notify-osd.

Notify-OSD has a specific philosophie behind it. Which is the same excuse the people quoted in this article use, but well. Notify-OSD tries to show these notifications and make them ignorable.

Software like pidgin show a constant stream of background-noise. If every notification has the affordance to get clicked, or closed, this gets annoying very fast. By making them not clickable (and probably by that black design), they become easily ignorable if one is focused one specific task, but they remain to deliver some awareness what is going on. See https://wiki.ubuntu.com/NotifyOSD#Rationale

Thing is, that works. I can't tolerate moving pieces on my desktop and I always got highly annoyed by the notification-bubbles from before notify-osd or when the daemon fails to start or from Windows. But the black unintrusive notify-osd-notfications i can stand. So for this example, not following that users' wish follows not only their design, but also the wish of users like me.

If a notification requests response buttons, there's a fallback to a basic dialog box, that doesn't look anything like the regular Notify-OSD bubbles. Ubuntu discourages using that, but it does work.

Maybe I'm misunderstanding, but how? I thought that the interface for notifications was just to provide some text and maybe an icon.

You can also have action buttons in notifications. See, for example, http://minus.com/lbpCsG which is a minimal MPD client written as a notification for gnome-shell. In gnome 3.6, you can interact with it using only the keyboard (<Super>M, left/right to select the notification, up, left/right to select the button and then enter to activate it), which you can't do with the usual status icons unless the app is programmed to behave like that, and which I think you can't do either with indicators like those used in Unity (though I haven't used that in a while, so I might be wrong).