We just built the regular size staunchion for our pygmies and it worked just fine. The only thing I wish is that it was taller. I say that because we use it for things other than milking.
When you want to trim hooves, look at udders, worm, give injections etc you might want them restrained and sometimes reaching down that low while standing is a PITA.
If you're going to be sitting while milking a regular size will work just fine. Build it so your comfortable on your choice of seating height wise and then to regular dimensions. (Unless a dwarf has that much smaller a head than a pygmy?)
One lesson we also learned, don't build it with a permanently attached feed stand. The goats just always mess with it, always look for the food etc. Our goats took about a week to break it off. If you're building your own, build it so that you can get one of those hook on feed buckets to put on and tempt them through with/feed while you milk and remove when you leave.
Laney