POP3 does not have a way to sync, or change, a message's read/unread state.
Therefore:
1 - Mail apps assume that any new messages are unread
2 - Most mail servers / services will mark as read any messages downloaded over POP3, for the benefit of web mail and IMAP. This is completely server side and is automatic. Some mail services have a setting for this (in web mail), some don't.
Since IMAP does have read/unread state sync, you're seeing this automatic "mark read" propagate into Aqua.
The best way to access a mail account from multiple devices, be they mobile (Android) or not (desktop) is to use IMAP everywhere.
You'll need to add your account again into Outlook (no way to change between POP3 / IMAP for an existing account), and use some sort of Advanced / Manual configuration step, so it doesn't default you to POP3 again. Once you know it's working, remove the POP3 account from Outlook or just keep it from checking mail (I believe there is a per-account setting for that in Outlook).
I'm not an expert on Outlook by any means, so really can't advise in more detail.
After switching Outlook to IMAP, you'll have access to server side (web mail) folders there, and also the read/unread state and star markers of all messages will synchronize between AquaMail, Outlook, and web mail.