It took a while to find this method, and it’s only part-way there (no minimise to notification tray). I thought maybe it could be made much easier, like the Browser Integration add-on does a variety of good things for Firefox, but i really don’t know, i’m not a developer or engineer.
In the Thunderbird settings, under General - Config editor (all the way at the bottom of the page) there is an item called: mail.biff.show_tray_icon_always which is set to false. I double clicked it and restarted Thunderbird but that did not change anything so I reverted to the original value.
I must say I have no idea what mail.biff is but I was hoping it would give me a tray icon.
Fyi, I’ve been using birdtray to do this for years. Would be great if thunderbird finally supported this officially (I’m kind of reluctant to switch to betterbird, too many weird firefox forks burned me in the past) but so far birdtray has been doing the job well enough for me.
It was removed after they found issues with the flatpak or something like that, and nobody fixed it since (at least since I last checked).
Correction: it wasn’t flatpak specific, I was mistaking it with Cinny where the problem was that. In Thunderbird’s case it’s just general issues. 1942125 - [meta] linux sys tray icon issues
Yes, I kind of forgot about that (because it’s been working without issues since setting up), you’ll have to run Thunderbird through XWayland to make it work, there’s issues in the birdtray github repository with more information, but basically birdtray has a setting for the thunderbird command line which you just have to set to /usr/bin/env GDK_BACKEND=x11 /usr/bin/thunderbird and then make sure to always start birdtray instead of thunderbird.