>> Outlook will mark as read the messages it downloads from your server. Please look into Outlook settings in order to deselect the option marking downloaded messages as read (I don't use Outlook myself to tell you exactly where to find this option).
No, no, no.
It's completely different.
If you have AquaMail using IMAP -- then it will sync read/unread state from the server.
And if you have Outlook using POP3 -- then most mail servers will mark any retrieved messages "as read", on the server, which will then sync into AquaMail as read over IMAP.
BUT
Since POP3 doesn't have read/unread state sync -- your messages will show as unread in Outlook.
Remember that mail apps don't sync with each other -- they sync with a central place, your mail server. And sync capabilities are different between IMAP and POP3.
So it would be much more relevant to check how messages appear *in web mail* (the closest we can get to "on the mail server") -- after Outlook fetches them.
If my theory is actually right, and the issue is the mixing of POP3 with IMAP -- then I recommend switching your account Outlook to IMAP as well (I think it's can only be done by re-creating the account). IMAP is the preferred way to access same mail account from multiple devices / apps, be they mobile or desktop.