I had a talk page message on some small wiki, which resulted in a global notification, the badge became blue. I looked at the notification panel, but neither opened this talk page message nor used the .oo-ui-icon-close button (which btw doesn't have a title attribute, so I'm not completly sure what I'd expect from that button anyway). So the badge became grey again and still said "1".
Now I got another talk page message (well, more like a few months ago, but the notification wasn't globally visible until shortly) and the badge stayed grey, the counter increased as expected.
I'd expect the badge to become blue again, as it would if there were no "seen but not read" notification left. Imagine a notification from "totally unimportant wiki" first, and a notification from "more important but not-so-often visited wiki" after that. --~~~~