Preferences - Incoming Mails
[x] Show an alert
[x] Use the system notification

The rest of options are unchecked.

When a new email arrives and Thunderbird is not focused, the new Windows 10 native email notification is displayed (ok), but it disappears from the Action Center in a few seconds. It should stay in the list of notifications in the Action Center until the notification is either clicked there or the new incoming message is opened in Thunderbird.

Now you will lose the new email notification information at all because it automatically disappears in few seconds.