That's what I thought but I was wrong. It doesn't
make any difference which way the rod goes. The correct way is with the shinier end with the shorter nib and the beveled shoulder pointing into the booster. The small inner piston cap piece with the dinky o-ring is perfectly shaped to fit it that way. However, the receiving end of the primary master cylinder piston is basically amorphous, not shaped to receive anything more defined than a simple spherical end. The length of rod sticking out of the back of the MC piston is the same either way, and the rod will fully seat in both pistons regardless of orientation.
I'm beginning to think that there might be some difficulty in assembly as far as getting the inner piston to seat down in the bore fully while the springs are installed???