Sorry for the dumb question but can Claws poll for new messages without having the entire app running in the background like Modesty can do?

Cheers.

Looks like it doesn't. The closest thing apparently is through invocation from term.
http://linux.die.net/man/1/claws-mail
But this still launches the whole thing. There's an --exit switch but I don't know how to make it launch when claws is finished checking mail.
Then there's the issue of getting it to play notifications properly. Mine doesn't play a sound even when I explicitly tell it to do so (notification plugin).