I'm saying the inquisitor's worldview is incoherent because he's not an atheist. So he's deceiving himself. His rationalism is arrogant in the face of his assumption that there are divine powers at work. If there's a devil, there has to be a benevolent God. (Actually, there doesn't, but that's the Christian context.) So the inquisitor may be sincere, but he's confused. An atheist with a coherent (but possibly false) worldview wouldn't concede that someone is the second coming of Jesus.

I think the inquisitor may be trying to make the best of a bad situation. Religion caused that situation, and cynical social engineers have to fix it. But the social engineers don't delude themselves into thinking that their Machiavellian calculations have a happy ending. The situation can be patched up but not perfected by such cynical masters.

In the NT Jesus performs miracles, but they were minor relative to what he could have done. That's the inquisitor's point. Jesus could have conquered the world so there would have been no need for a second coming. Jesus could have been the messiah the Jews wanted. He could have defeated the Roman Empire.

Dostoevsky's theodicy is that by sending only a spiritual rather than a warrior messiah, God preserved people's freedom by withholding overwhelming evidence. The miracles might have been overwhelming at the time in those areas of Judea. But after millennia we're left with only written stories which can be easily disbelieved.