For convenience, I think that notching the top board and placing the scale bewteen the top and ground board has one significant advantage.

By doing it that way, you can place the pointer in a position that rotates with the focuser - the natural position for the observer to be in while at the scope. You can always see the pointer without moving around the scope.

By placing the pointer on the ground board, there will be times when you have to walk around the scope to see the pointer and then return to the eyepiece. Not quite as convenient.

Having said that, both systems will work, and nobody should let this issue prevent them from putting this system in use on their scope. Just do it in whatever manner fits your idea of convenience, your skills or your whatever other preference you might have.

Good Luck