Each board will have slightly different measurements, they are not all cut the same, it just means that they have a set max size and a set screw location.
ITX is the smallest size, you also have to do addon cards if there is any, power supply, you need standoffs for the motherboard so it does not short out, you need decent bays for hard drives, and you need airflow. Whateve the gamecube has in it is not enough for pc components.
In all reality you will spend way more then $40 (cost of cheap ITX case) plus hours and hours of time to do this (and you will need some decent fabrication skills to pull it off)