AdamM Both protocols have to be generally configured for automated deletion. POP3 was originally intended for message retrieval and deletion from the server, but then the plethora of devices with each connecting to email was the problem and IMAP was developed and intended to be more of a client / server solution.
IMAP allows for easy deletion both from the server and local while POP3 generally deletes from local storage and leaves the message on the server unless deleted at retrieval which would have been generally automated in earlier days, but both protocols generally need tweaking in email clients to automate deletion from the server and keeping email storage in the client. That's been my experience anyway. These days both seem to work about the same way but IMAP idle gives you more of a push email feel and the client / server nature make it more obvious to delete individual emails or a partial range from both sides.