Do you have access to any of the college libraries? It would be great if you can peruse the entire article. The paper goes more in depth on the studied functions of micropits. And, the micropits don't just receive signals from the pit holes either as they are found all over the head and body of the boid.
Finding the head in the dark tells us a lot about the infrared image the snake is receiving as striking in the general direction of the rat may not tell you what the snake "sees" but more what the snake hears/feels. So, if it can still target the head of the rat with that thin beta-keratin layer over the pit membrane, then it's an indicator that the absence of the visually-normal pit holes is not in any way providing a handicap.