It just does it super fast. You are shown the 2nd-to-last card, the game recognices there is no choice for you to make (put it on top or bottom is the same) and speeds things up by making that choice for you.
In the log file, you can see what happend.
Here. I did a quick bot game:
Turn 8 - WhiteRabbit1981The last card in my deck was a chapel.
W plays a Pearl Diver.
W draws a Pearl Diver.
W looks at a Chapel.