Alamo: very interesting set of charts! Thanks for putting them together!
Jason scoring is set up so that milked games don't always dominate the scoring tables. The key is to reach Domination limit rapidly; from that point on, milking might gain you a bit, but isn't overpowering. The issue is that most players don't milk, and many don't reach Domination limit. For these players, the longer the game lasts, the more this 'milking reduction factor' impacts their final score. For this large group of players, it's no surprise that Spaceship submittals score lower as a group than Diplomatic submittals; they haven't had a comparable increase in score to compensate for their longer game.
Happiness does impact the milking score. In my one Histographic attempt, turning on the Governor (to handle Pollution) gave me an immediate 10% reduction in Firaxis score gained per turn. Many of my Entertainers were turned into Taxmen or Scientists, converting some Happy citizens to Unhappy. Stupid Governor!
It would be interesting to hold a Histographic target victory condition game, get lots of Histographic results, and correlate final Jason score with date that Domination lmit was reached and approach to milking. (Or we could read posts from certain players, and know how to milk correctly, in theory.)