Yes, the preload on the spring affects the measurements you'll get on the others. However, don't get caught up on that. Race sag is the important one you're shooting for.
I would start with 10mm of preload on the shock spring and then measure your race sag. Once dialed in, normally 105mm is a good starting place, check your static sag to know whether you have the correct spring installed or not. You should be able to go from 100-110mm of race sag and the static sag (spring rate) still be within range.
Lastly, I wouldn't run the fork tubes flush with triple clamp. I imagine you're getting some push in the corners no matter what you do with the clickers yet is very stable in a straight line/high speeds, yes? Normally setting is 5mm above the clamp and adjust from there. I'm currently at 8mm above and running 105mm race sag rear.
I know this is for Kawasakis but the same principles apply to our Gasser/Rieju bikes and is how I learned to do it correctly.
