Yeah I know the functional reason for aligning the tire logo to the stem. I did it on my old tires, but those tires had the tire brand and model name stacked one above the other on both sides, so alignment was easy. I just aligned it to the Continental logo because it's yellow and easier to see.
On the GP4S the graphics alignment extends from the Continental all the way to the Vectran at the other end. The center occurs somewhere between the I and the X in "PRIX". Maybe one day I'll move the tires around and center them there.
Oh and I LIKE the retaining nuts personally. Too often I've had to deal with the stem pushing into the rim when trying to attach the pump, and generally just being a PITA.