You can see the integration between Publish and AF 4.0 on my site, www.lawsonguru.com. (you don't need to register/login to see the forums, but you do need to register/login to see the articles).
Publish categories are linked to AF forums.
Here is an example of an uncommented article (see the 'Be the first to comment on this article' link at the bottom?):
http://www.lawsonguru.com/tabid/158/itemid/118/Deleting-a-GL-Budget-via-Excel-AddIns.aspx
When the user comments on the article, the article description and a link are added as a forum post, and the user's comments added as a reply to the post. I'm very happy with the way that works. Note, though, that the integration is "one way" from Publish to AF. An enhancement I'd like to see is to be able to associate an existing article with an existing Forum post.
Here is an example of an article comment, from the forum perspective:
http://www.lawsonguru.com/Forums/tabid/96/forumid/1/postid/5369/view/topic/Default.aspx
and from the article perspective (see the 'Discuss this article' link at the bottom?):
http://www.lawsonguru.com/tabid/158/itemid/162/Uploading-to-Asset-Management-using-Lawsons-Excel.aspx
You are correct--the comments to a given article are not visible on the article detail page, only in the forum.
I agree that it would be a wonderful enhancement to be able to inject some of the forum comments into the article!
I'd also like to see the number of comments as well as be able to move the comments pane up within the article.