What you are reading when you have the insert sitting flat on the counter is the 1/8th reverse of the top edge of the thumb mold. When you make a mold of your thumb, it takes into account all the bevel and pitch of the thumb in the ball. When you create the mold and have it centered into the cylinder to make the mold, it will mold all the bevel and oval of the thumb but not the pitch. If you took this mold you made and inserted into a ball that has 0 and 0 pitch, the leading edge of the thumb mold will stick up while the back edge will be flush with the surface of the ball and if you go and trim off the access and put your pitch gauge in this thumb, it will read 0 and 0.
I ran into this problem when using the Vise Exactacation system. I would make the mold fine, but when I inserted the mold into the cylinder to make a copy, I would have the cylinder flat against the table and the bottom of the mold, the "head" as Brunsnick calls it on his website, would be all the way in the cylinder. This was causing the pitches to go all wacky and when I would drill the ball to the specific pitches and installed this new insert in, it would produce the wrong pitches. I was corrected by another driller who has his own system but its hard to come by.
Hope that clears things up.
Roto4ever