I'm pretty sure the problem is JoomlaComment and the way it's coded. I don't think it's Daniels' doing, because he took over the component from the original creator - and never redesigned the plugin as far as I know - but it inserts itself within the com_content body - it 'hooks' into it sort of thing - and other plugins have no way and no idea to see the difference between the article text and the Comment system, it just sees them all as one thing - the content.
That's... just my own words, so take it with a grain of salt. It seems to make sense though, but I've only read the Joomla dev docs and thread after thread on specific things, and just have a long background in legacy scripting but PHP is relative new to me and Joomla is VERY new to me...
Ahem, I digress. I really haven't had the time to sit down and actually read or do training in Joomla or Web Development, I lack patience and still have my day work to do... but I really should, because it annoys the HECK out of me that I can't solve this seemingly simple issue...
...well that was a rant, sorry about that haha. Yeah I'm still trying some things, you are lucky to catch me at this time because I'm very interested to figure this out myself - it'd be good Joomla knowledge - I bet Daniel knows straight away what to do, but I'm not sure how long until he arrives home.
We'll figure it out.