Sorry, the title is a bit confusing so I will explain.
I want to allow comments on replies but NOT on the original question. But if I go to Settings --> Comments and set "Enable Comments For Questions" to NO and "Enable Comments For Replies" to YES then the system does not allow me to comment the replies. When I click submit I get a message about needing an account to be able to comment.
Please take a look for yourself. Right now I have comments enabled for both questions and replies and it works in both. But go in to admin and set "Enable Comments For Questions" to NO and then try to comment on one of the replies and you will see what I mean.