M6 hole is for the screw that holds both parts together (see matching counterbored hole in lower part) as mentioned on P16 and illustrated in photo 8.
By reducing the height to 19.5mm after machining the hole makes the hole more or less oval so the cam can force the two parts apart.
I guess the M3 hole is for a grub screw to lock the screw that holds the two parts together in place, once you have it in adjustment.
Afraid these sort of details are easy to overlook when editing, easily spotted if you actually build the thing.
I might mention this in Ed's Bench.
Neil
Edited By Neil Wyatt on 08/03/2016 18:48:34