Yeah I know, that this is done this way, but I have asked for an "work-around". But I think there's no possibility, because the pop command will download all mails to the server and then this will get deleted. Perhaps if they (devs of phplist) would code something like imap for bounces and add a code behavior, that only mails, which match the rule "xyz" will be deleted and not the whole box.
Will look for another setting, if this could work.
// set this to 0 if you want to keep your messages in the mailbox. this is potentially
// a problem, because bounces will be counted multiple times, so only do this if you are
// testing things.
$bounce_mailbox_purge = 1;
// set this to 0 if you want to keep unprocessed messages in the mailbox. Unprocessed
// messages are messages that could not be matched with a user in the system
// messages are still downloaded into phpList, so it is safe to delete them from
// the mailbox and view them in phpList
$bounce_mailbox_purge_unprocessed = 1