Apparently this was made to display Flow updates in the "messages" icon, which is lower priority and less emergency-looking. However, I disable Flow notifications, so I now have:
- the highest priority notifications possible (messages in my user talk) in a lower priority queue;
- the low priority notifications (mentions, thanks) in the high priority queue;
- the lowest priority notifications (Flow stuff from random watchlisted pages etc.) correctly hidden (I hope).
This situation makes no sense at all. The easiest solution would be to restore the single-icon setup if one ignores Flow notifications. An alternative solution would be to rethink the whole "feature".