IMAP and Exchange have a feature what the read/unread/starred state of each message will sync between the app and the mail server.
POP3 does not provide this, so each mail app tracks unread messages on its own, and will mark as unread any "just received" messages.
And when you use a mail app that is set up to use POP3, then most if not all mail services will mark the retrieved messages as read. And then those messages will sync as read into AquaMail if you're using IMAP or Exchange.
The best way to use multiple email apps is IMAP or Exchange (but Thunderbird doesn't have EWS, only with a third party extension).
Second best is to use POP3 everywhere, but you won't have folders or push.