In short: This is by design.
At a simple, intuitive, level, as you noted yourself, - these messages are not part of a conversation. Right?
So, through a magic, Aquamail doesn't put them together as a conversation.
(The only common things between them are the (automated) sender and the subject. Yes, one can consider that makes a "group", but not a conversation.)
At a technical level: while some other apps, Gmail included group messages together based just on the subject, Aquamail doesn't do that. It relies on the internal reference(s) that are created when a message is sent as a reply or as a forward. Those are reliable signs of a conversation.