It's highly doubtful a priest would let Stefano, or anyone for that matter, stand on altar (which is sanctified object) to examine the painting, as he does when he arrives.
When Coppola takes a leak, it's too short amount of time for urine to even start coming out but he is already finished.
When Stefano leaves Copppola, mid-conversation, to check on Francesca, when he finds her sleeping, he returns momentarily to find Coppola gone without warning or trace. He then goes outside to look for him, and hears the front gate slam, assuming most likely that Coppola had left without saying good-bye. End of scene.
Next time Coppola appears, he offers no explanation or apology and Stefano doesn't bring it up.