Mother Superior doesn’t get the last word? Doesn’t she correct Homer and remind him that He, meaning God, was the builder? It’s kind of the punchline for the whole story.
The punchline is the title. She wins his ascent to working himself to death on her projects for no pay by having him read the passage in Mathews account of the Sermon on the Mount.
Jesus preaches not to worry about money—something Smith wants in return for his labor—because the lilies of the field don’t worry about anything, and not even Solomon was as richly arrayed as they.
On your point, however, just who is in charge of everything is the delightfully dubious aspect of the film that the viewer must resolve for him- or herself.