They are worried about someone copying a mistyped email from the first form field and pasting it into the "confirm email" field, thus making the confirmation field pointless. I would suspect in the real world most people are typing their email by hand and not using a password manager or auto-fill so this becomes an actual problem.

A nice implementation of this would detect that you pasted/auto-filled the original field and not prompt you to confirm unless you typed it slowly by hand.