After looking at this for a few days, I was finally able to hack together a solution. My feed now uses the results of get_content() instead of just $p->post_content (which isn’t processed by the filters). Unfortunately, I wasn’t able to preserve the ability to change this with the Diamond formatting string, but at least it works!
It would be nice if the plug-in were updated to work with the filtered contents and include comment info in the custom feed.