Dude, did you miss the entire scene of Jonah venting in private to the big crucifix after Boyd got healed?
The guy was SEETHING, unable to control himself anymore. All that "true gospel" that came out of him (saying how love never started, how meek get screwed and no one is innocent) felt 100% true (there was no audience to con).
It makes sense that his being abandoned story was 100% true, and he clearly resents God for it (parents are our closest image/example of God).
Meaning if God truly cares (enough to heal Boyd), why was he deaf to Jonah's pain when he needed help the most and did not receive it?
Better to think God doesn't exist and put it past you than to realize he does exist, and you were rather ignored, made to suffer in vain. That is the gist of his rage at that point.
Al's got it right on the money. That part of his life is likely to be true, because the best lies have a kernel of truth in them. Also, that is my favorite scene in the entire film.