I have just setup WhatsApp web add-on to Thunderbird, when I noticed that if I tried to enable desktop notifications, it wouldn't work. So I looked at the GitLab page for the add-on and saw that Thunderbird does not have a prompt to allow Desktop notifications.
It states that there is a setting to automatically allow desktop notifications for everything, meaning that I would get notifications for WhatsApp, but I would get notifications for any other website I visit on Thunderbird, which isn't ideal.
I think it would be a good idea to add this prompt into Thunderbird so as to allow add-ons like this to send desktop notifications.