I'm with ya except for the "in the springs" position.
Droop, the downward travel of the suspension arm, is set with "0" blocks beneath the chasis and the guage beneath the hub [some even argue whether the shocks should even be on or in place when setting the droop].
Does the upstop [I realize most don't actually use this or it's a setting that most set as "free"] change with the tire diameter as well? Again, the measurement is made against the chasis.
What I've started doing is setting up & down stops without the shocks, note it and then make a note of the travel distances with the shocks in place. I use it more as a comaparison between runs, giving me a quick reference with the gauge while keepign the shocks in place. If I note a difference, then I know to slap on the the set-up station plates and all the other tools we use to se what changed and hopefully figure out why [usually a plastic-molded piece that allows a a screw/set-screw to back out or go in].
But what I'm I talking about? It's an Xray, settings never change unless I launch myself out of the track, in which case, I'll have bigger problems.
I'll check the settings with different tires diameters and see if I notice a change in up/down stops and report back to ya!<saluting with a commanding "Sir" coming out of the mouth>
^5