Hey Sean,
Sorry for the delayed response. I'd suggest reading this other post, we just did, which may help explain a little bit about the unique IDs we use and how to best use the JFBContent module vs individual tags per article:
www.sourcecoast.com/forums/topic?id=1745&p=1#p7466
With that said, some more specifics to your post.. If the comments are the same for each article in a blog layout, that's not right. We should be including a unique ID for each comment box. We'll look into it, but let me know if that's what you mean.
As for the Like button that is inserted using the JFBConent plugin can be disabled. Go into the parameters for that plugin and set it to hide. There's some other options available there too you might like.
Hope this answers most of your questions. The dynamic URLs can always be a problem, and we realized that when we first released all the social modules. The Content plugin was our first stab at correcting this, for articles at least, by always using the same ID regardless of how the article is shown. If you have any other feedback, suggestions, or questions, just let us know.
Thanks!