These days, using the OS's native notification would be a lot nicer than the bespoke Reminder windows Thunderbird uses. Also, it would remove the confusion when they're both used for different thing in Settings.
Yes, and the OS remembers earlier notifications too, and you can mute, manage etc all notifications from one place (eg switching on focus mode will have an effect on TB's notifications as well).
Certainly, it is more efficient to use the OS's native notifications for centralized management. But beware of big tech (Google, Apple, Microsoft, Meta, Amazon) that essentially collects and profiles user data. I believe that Thunderbird should be completed as native. Since users have diverse tastes and values, it would be nice to add an option.
I agree this would be a great option to add. I've been looking for months for a way to do that. I even tried learning how to create a Thunderbird addon that catches calendar alarms to send them to the OS notification system (if anyone has any suggestions on how to do that, I'll take them!).
Why not give the functionality of Reminders to Notifications and vice versa? Under each alert type ("Reminders" and "Notifications") in settings, have an option to select a global setting, a per calendar setting, and/or to go by the alerts you have set per alert. It would also be good to better signpost what each alert type does (a Thunderbird popup window for Reminders and a system notification for Notifications) in settings for new users.
I'd really love to see this, as well as being able to turn off notifications for email accounts. I'd like to only receive notifications from calendar, but not from email.