408 Cam on the way

Thanks.
I have RHS heads (closed chambers).
I'll have to get with the machinist who sold me the stroker kit and pistons. I should not be doing any milling. The machinist has already balanced the assembly.
Am I correct thinking if I am to calculate compression using the manufacturer offset of 25 cc, I would measure from the rim below the step up?
If you shave the tops off those pistons will you have the rotating assembly re balanced?