Well that is baffling. You are certainly doing a nice and thorough job.Well bottom line...both tools yield the same results. I think the slight variances actually came from slightly different preload settings.
I did make a small observation though which is a bit unclear, the manual does not specify whether the spindle center procedure where the tool is placed on the knuckle for the second scribe mark should be done with the turn lever installed. I have left it in place so the measurement is true to how it was oriented on the knuckle ball. The fsm drawing however, doesn't appear to show it in place. If it's removed, it will change the distance of the two marks but I believe it will actually bring them closer together decreasing distance D.
It occurred to me that a little handle some how attached to or a behind the scribe point would compliment the design of the tool.I did mine once also knuckle swap using Toyota tool it was a pain in the butt to get consistent readings had negative readings also looking at all the components and such I realized the tool was a slopping fit in the brass spindle bushing which was allowing the scribe mark to move wasn’t Centered in the bushing I also got it sorted in the end with no leaks. I’d have to see if I kept my numbers. Took me all day to get what I thought was correct I also grabbed nice new shims from Toyota.