Menu extras were never intended to be treated like Windows tray items. For the earlier portion of OS X’s life, there wasn’t even a public API to create them and required a hack and a private API, and the current API is intended for ephemeral menu extras that disappear when their host app isn’t running. In short, the menubar isn’t designed for users to collect menu extras like Pokémon.

But that’s exactly how it is used, and them disappearing behind the notch feels like a bug.

Sure, but for twenty years that’s not how they’ve been used.