I am also confused by your steps in the mash schedule, but I think I understand your point.
Once that initial water has been added and the water to grain ratio set, then the program considers all water addition in the subsequent steps. On the surface, one might say that this skews the perception of water to grain when steps are considered. Unlike a single infusion mash in a mash tun where the water under the false bottom and not in contact with the wort would only passively participate in the mashing process of solubilizing the starches and enzymes only through the osmosis of the fluids from the grain basket into the water below, the Grainfather has a pump which recirculates the fluid bringing it all into contact with the grain bed. Additionally, with such a device, temperature steps would be done through that recirculating system and not with subsequent infusions of water. I think this is what is confusing about the mash profile as it comes up. Your steps are numbered 2. Saccharification, 1. Strike, and 3. Mash out. Ideally, you would add the water and then strike with the grains initially at the lower temperature, then after suitable rest, bring the temperature up using the Grainfather to saccharification temperatures. No additional water should be needed and the calculation of water to grain ratio which excludes the water under the mash pipe only comes into play at the initial water addition.
The fact that the subsequent water to grain calculations uses the water under the mash pipe in subsequent mash steps is really immaterial once you start recirculating it.
