I've noted this issue. At the moment, it's possible to move messages retrieved by different identities, but not by different POP3 definitions. It would be trivially easy to inject a header into downloaded messages that indicates the definition that retrieved them: this header could subsequently be used in expression filters to do the type of thing you're asking for.
I'll definitely add this to the next release for you. I suggest that once you see blogs or discussions here indicating that full development is operational again (once I have finished the internal transitions that are happening at the moment) you send me a personal message to jog my memory.
-- David --