Still, if you’re like me, you may lean more heavily to one side than the other. In this regard, Scott Ellis’s production for the Roundabout Theater Company has not yet reached the ideal balance; Ryan, stepping in for an ailing Tyne Daly, has had just a few weeks to prepare. Her take on Aloysius is smart and uncompromising but a bit small in crucial moments, leaving the splendid Schreiber — a strapping 6-foot-3, with a tough guy’s brush cut and a thick Bronx honk — to outman her. (Brian F. O’Byrne, who played Flynn in 2005, was scragglier, and Cherry Jones, as Aloysius, more imposing.) Schreiber is also about the same age as Ryan, not a couple of decades younger, as written.

The climactic scene between the nun and the priest, as their certainties finally collide, is thus slightly muffled in this production, which doesn’t take enough time to let the momentousness of what’s happening sink in. In truth, that’s also a glitch in the play’s joinery: Something has fundamentally shifted, but Shanley refuses to say what it is. (A crucial coda is still to come.) I think this glitch is why some critics have found “Doubt” a bit slick: Like procedurals, it withholds information to maintain suspense, but unlike them it does so permanently. It’s manipulative.

Is that really a criticism, though? I want plays to manipulate me, and it is often truly the case that we cannot know the truth. For a man like Flynn, who has “things he can’t say” in 1964, it may well be that he is innocent of Aloysius’ charge but guilty of something else.

Such ambiguity, necessary and humbling, is an enduring concern for Shanley, who is the subject this winter of an accidental New York retrospective. The same unsettled judgment lies at the heart of his more directly autobiographical “Prodigal Son,” in which another troubled boy — played, in its 2016 Manhattan Theater Club premiere, by Timothée Chalamet — comes under the sway of another Catholic mentor. Underage drinking is again involved, and also sexual impropriety.

Still, Shanley does not quite condemn the teacher in “Prodigal Son,” modeled after a central figure in his own youth, except in using his real name; moral inquiry, the play demonstrates, is not the same as moral certainty.

Nor is it the same as moral inconsequence; some people do pay for their sins. As I see it — your takeaway may vary — “Doubt,” in this production, throws Aloysius under the bus for her pride. That seems realistic. The Father Flynns of this world often bounce back from much graver accusations, not because they are necessarily innocent but because, with a collar or not, they are men.

Doubt
Through April 21 at the Todd Haimes Theater, Manhattan; roundabouttheatre.org. Running time: 1 hour 30 minutes.