I could see it working a bit better if the original podcast had fixed points where they allow comments. So they can say something like "ok now we will open this section up for comments, and afterwards we'll continue on to...".
Then as comments come in they can follow a dialog structure, or the original poster can come in and add some clarification as a reply.
edit: If there are a lot of comments coming in, you could set it to autoplay only the top X comments and their replies or whatever.
For reviewing afterwards, it would also be really helpful to have an auto transcription so you can quickly scroll through for anything you missed or want to go back to.
Then as comments come in they can follow a dialog structure, or the original poster can come in and add some clarification as a reply.
edit: If there are a lot of comments coming in, you could set it to autoplay only the top X comments and their replies or whatever.
For reviewing afterwards, it would also be really helpful to have an auto transcription so you can quickly scroll through for anything you missed or want to go back to.