There needs to be some provision for adding a comment to a checklist item. For example... if a checklist item is not applicable then the author or moderator could check the item and add a comment tha...
This would be helpful for us as well.
Last year when I asked Smartbear about this though, they mentioned that they've had the request quite a few times before, but at that time, management decided to keep to having only the two states on the checklist, no comments.
In the case above an aditional state of -1 could help, but looking at the database (reviewchecklistitem) the state is char(1), so adding other states should be possible - though not sure about the gui client code.
As for the commenting part itself - I was advised to just add the comments to the general section, which probably won't be ideal as you may sometimes have a lot of noise and discussions going through there.
Not sure about the underlying complexity in the GUI code, but they should be able to add comments *against* the checklist items at least. The events seem to be stored in reviewchecklistevent, so really only need a text field in there to be populated.
You won't always want to change the state of the button when you add a comment, so they should really be independent from each other.