Thunderbird 78.7.1 (apt version) running on Ubuntu 20.10 with default Gnome desktop. I don't get pop-up notifications when new mail arrives, although I believe I configured it properly. Thunderbird is running, minimized, and Birdtray shows new mail items, but no pop-up notifications. I do get pop-ups from Gmail in Firefox, so notifications are working on my system, but not from TB. See screenshots.
Install
thunderbird-gnome-support
Now Thunderbird notifications integrate well with Gnome desktop and Gnome notification center.