As no one responded to this, I bought a few sacrificial rolls of cheap film to experiment with (Lomography color print film is apparently the cheapest film available in 120). It turns out that the little window on the side is a frame counter. To get it aligned you load the film and then advance it until a double headed arrow on the backing papaer labeled "Start" lines up with arrows on either side of the frame gate, right in the middle of the frame. Then close the back door and turn the advance knob. The frame counter advances to 1 and then the advance locks. To advance to the next frame there is a little button below the frame counter that you slide down. I had never had reason on any other camera to advance the film that far before closing the back, but it would seem necessary that all brands of film have some sort of "Start" indication.
I have to assume that other TLR's use a similar mechanism. To use a ruby window, either the pressure plate needs a hole (or holes) in it or there is no pressure plate at all. I did check the accuracy over the length of the film and it does appear to err on the side of caution, going just a smidge beyond the number on the film back with each advance. This shouldn't be a problem given the length of the film. What did surprise me is that the frame counter was accurate enough, especially given the complexity of 35mm with the sprocket holes and wheels, or the Kodak Medalist that used a combination of a ruby window and a frame counter and you have to hold your mouth just right to get everything aligned properly.
If it is that easy to make a frame counter for 120 film them why did so many camera manufacturers stick up with that PIA ruby windows for so long?