The idea is that by minimizing the water you can maximize the starchiness of the water, which creates a great emulsifier for the cheese sauce, along with evaporated milk. The combo is truly creamy mac and cheese, with no grittiness or separation of oils. It tastes great, it's faster than Kraft, it's energy efficient, it's easy to learn (literally 3 ingredients plus water).
It also has easy-to remember-units (6 oz pasta, 6 oz cheese, 6 fl oz evap milk). The evap milk amount perfectly divides the USA standard 12 fl oz evap milk can.
Kenji has tweaked the ergonomics of scratch mac and cheese light years ahead of where it was.