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Are there any plans for tray icon and desktop notification support? Those features are the only reason I would run a desktop email client, without them I'll just use a browser. I know Birdtray exists but I can't get it to work with flatpak Thunderbird.
There may be solutions for your issue. https://github.com/gyunaev/birdtray/issues/514
Maybe try birdtray flatpak or using the special launch argument as described in the link from the comment.