The top and bottom have almost identical circuitry, even though the layouts look entirely different. The layout of the ALU is highly optimized; since everything

The top and bottom have almost identical circuitry, even though the layouts look entirely different. The layout of the ALU is highly optimized; since everything is repeated 16 times, squeezing out a bit of space makes a big difference. I assume the layouts are different due to the surroundings: The top stages have two bus wires next to them, while the bottom stage just has one bus wire, so there is a bit more room. Some of the horizontal metal wiring is different (like the wiring in the gap you saw), and power and ground may be offset slightly. The top stage needs to fit with the register interface circuitry just above it. My suspicion is that these relatively small changes resulted in the layouts being visibly fairly different. Maybe I'll do a gate-by-gate comparison at some point to check.