Yes, the blue line labeled "aluminum piston with cup" is with the stock valve...meaning the end of the valve is the original conical shape that matches the rubber cup.Only the red line labeled "aluminum flat top piston" has both parts modded...meaning they each have flat faces so they meet with minimal headspace.
The volume of the valve is unchanged in Bob’s comparison so we can see how much pressure is achieved with X number of pumps depending on the type of piston and head geometry. If any of the configurations had a different valve volume, we could not directly compare them in this way. Incidentally, in most cases you would not want to increase the valve’s volume. Perhaps you might for a 13xx that has been retrofitted with a long .22 barrel but it would be counterproductive for a short barrel in either caliber. It would just take more pumping strokes to build the same pressure yet it would yield no benefit…just louder because the valve would be belching air well after the pellet has left the barrel. Some folks have actually gone the other direction and inserted something in the valve to reduce its volume so it takes fewer strokes to build pressure. From my perspective, the big takeaway from Bob’s excellent study is that there is a massive benefit to using a stiffer piston and placing a shim of some kind behind the pump cup to take up any headspace (make it so the cup squeezes against the valve when you close the pump arm). At anything up to 10-12 pumps, there’s no need for a flat-top piston or valve. For example, we can see an almost 50% increase in pressure over the OEM arrangement at 10 pumps. The reason that is appealing to me is because that’s about as much pumping effort as I’m willing to invest. I mean, sure it might be fun to pump 40 times and see the max power I can get. I’d do that once…okay, twice so I can see if it’s repeatable. But that’s about it. From then on, it’s never going to see more than a dozen pumps. Regarding your question about the poly tube transfer port, I think it had been established as a slight benefit for .22 cal and a slight detriment to .177.