I have read that this should work for comment threads, but no luck (at least not in my reader):
<link rel="replies" type="application/atom+xml" href="" />
<link rel="replies" type="application/atom+xml" href="" />
Accepts BBCode with a few enhancements.
I suppose if I dug around the RSS Bandit source code I could figure out an answer for you. I believe that it transforms (possibly through XSLT, but I’m not sure) all feeds of different types into its own internal format.
If you have a SourceForge account, maybe you could open a bug and see if you get a response. That’s how I found out I needed both the elements you mentioned for RSS to support comments feeds (which is odd since they’re part of two entirely different extensions to RSS and should not be both required).