I asked those same questions myself a while back here. As it was explained to me, the rotor design will work better with only two openings instead of three. with a center inlet you're hurting the effectiveness of the pins over the cpu by breaking up the flow through that area. (i'm not sure quite why, anyone?) As for the copper drilled top plate, there are two reasons for that. The first, and less important reason is that with a tec block (which a rotor block could be easily used for) there will be some heat that will be transferred to the top section and the pins on the top will help dissipate that to the coolant, but that effect would be minor. The second, key reason is for the added flow through the block gained by doubling the area for the coolant to flow through. which if you wanted to simplify things and use either a lexan or flat copper top, you could either make a slightly thicker base plate or just say screw it and accept the flow restriction to your system.
