It may be great that when one receives an email with an invitation to a meeting/event and reply using the buttons Accept/Tentative/Decline, the related email is deleted from the inbox.Outlooks has a config flag for allowing this behaviour.
Somehow related to this Windows issue https://connect.mozilla.org/t5/discussions/thunderbird-beta-115-unread-indicator-not-cleared/m-p/34574 where the tray icon remains active even if new emails are read.
Same issue here. Don't know if related to also the system notifications https://connect.mozilla.org/t5/ideas/dismiss-new-email-notifications-when-email-is-clicked/idi-p/29122
