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I was originally experiencing the same issue, but through some testing I disabled the Chrome flag which sends notifications to the macOS notification center so Chrome would use the old style default built-in Chrome notifications.

That has made the issue go away. It's not a viable solution as there's definitely benefits to the notification center generally, but I think it is pointing towards an issue there. I've also not been able to reproduce anything similar on Windows.

Hopefully this will improve over time.