Ideas for workarounds:
- Don't use IMAP Push, instead use sync every x min. So most of the time Thunderbird will be faster
- Let the server do the rule of marking as read (if possible)
- Ignore notifications of AquaMail, if you are at home. Notifications will disappear, when mails are marked as read
- Let Tasker and AquaMail plugin do the job:
Tasker can change settings and disable notifications of AquaMail, when you're at home (home Wifi)
Tasker can stop the notification, wait for x seconds/minutes, then show a notification.
Maybe one of the ideas helps?