I've kind of always thought the Madstad for the Gen II had you take off the the adjustable Gen II stuff to get back to a basic mounting point. Kind of strange to put an adjustable after market mount on top of an adjustable mount. Though I guess they would change the spacing so you still use the Gen II screen. Anyway, it's real close to 8.25" center to center over the arc on a Gen I screen.
You're correct, you do take off the OEM Gen II adjuster to use a Madstad adjuster. It's just that the "basic mounting point" as you call it, is the same on both Gens. So if you could buy a used Gen I Madstad with a screen for cheap, it will fit on either a Gen I or Gen II bike. That's likely what occured with the '16 bike here.
My Gen II bike came used to me with a Madstad adjuster and a HUGE barn door of a Madstad screen. I hated it and couldn't get the buffeting to stop, no matter how I adjusted it. I took it off and installed my Gen I Med CalSci screen on the Gen II and returned to blissfull smooth air.
In my case, the Madstad was a Gen II unit. The windscreen spacing was Gen II. The buyer of my Gen I bike wanted the MadStad adjuster, but not the barn door screen. The Gen II Madstad fit perfectly on the Gen I bike, but I had to drill some new holes in the stock Gen I screen to mount it to the Gen II Madstad adjuster. Last I heard that rider was still running that combo as it worked well for him.
If you wanted to mount a Madstad adjuster on an OEM Gen II adjuster, you'd have to modify the mounting holes on one of them to fit. Then use what ever screen the Madstad fit. Well, I suppose if you got really crazy, it's possible to mount the Gen I Madstad on the bottom and the Gen II Yamaha adjuster on top, then mount a Gen II windscreen w/o having to drill any new holes.