Answers to 2nd and 3rd question makes sense (made of fire vs made of clay and invisible). But the first one by the holy man makes no sense. In fact his argument ends up agreeing with the non-believer's point !
No the scholar is not agreeing with the non - believer's POV , he is telling the non believer that everything is not Mashallah. For certain acts Allah has given a free will to act.
See post number 29.