The Pediment

Above the door, a decorative semi-circular pediment is faintly visible—its edges softened by the deterioration of Leonardo da Vinci's Last Supper.
Interestingly, the center of the circle that defines its outer edge is not aligned with the vanishing point of the perspective. Instead, it sits slightly higher.
Within the circle are Jesus and two hands—one belonging to James the Greater, the other to Thomas, who points his finger towards the heavens. Notably, the head of Thomas touches the circle from the outside – without entering it.
Was this careful arrangement intentional?