I'm just speculating here, but it could be that he doesn't want to risk doxing himself. If he emailed them from his personal email address, which contains his real name, the journalist could out him.

It would be extremely counterproductive for a ProPublica writer to maliciously dox someone who pointed out a logical inconsistency in their writing, if the writer's intent is to bolster their own trustworthiness. Any journalist crazy enough to do this would be forever out of a job because no source would ever speak to them again.