Please visit our forums, we monitor them daily and can answer questions promptly regarding the PowerPress plugin. http://forum.blubrry.com/
1. Do you mean you want a flash audio player in the feed content? Any embeds in a feed are considered invalid according to feedvalidator.org. Further thought, most feed readers like Google Reader and even Facebook will strip these embeds out if they were there for security purposes. If your only reason for having a player is so it appears on Facebook, you may want to search Facebook for the Podcasting widget which displays a player with an integrated into Facebook player.
2. Discard HTML comments? I don't follow this question at all. PowerPress has nothing to with comments, that's all handled by WordPress.