It is common practice to setup a different subdomain if you want to keep the mail separated. The mail system within discourse can work with a completely different domain than where it is hosted. For example, I have discourse at forums.tld.com and mail at mail.tld.com. This allows my main mail server at tld.com to remain independent of Discourse’s mail management.
We just moved from the pop3 model to the mail receiver model. It was a very easy install and works much better.