Firstly, I do know and use the extension "Minimize on close".. and the "hide when minimised" tick box.
Yet I wonder why this still isn't a native feature in a programme that is clearly designed to always run in the background anyway.. At least since calendar and reminders are now baked into it, it just makes no sense to close the app completely and not receive these alarms.
Relying on 3rd party apps that sometimes just break after major updates is not great in this case, and make me reluctant to update (cause you never know what's gonna break).
I find this "always running" behaviour annoying with most types of software like Zoom/Skype/etc., especially if you cannot turn it off. However, for Thunderbird: please make this a native feature, but leave users the option to turn it on or off.