Wow. Your right . TPS really dropped the ball on that one
Pin 1 (closest to rear of board) is the input for the HDD Activity LED.with a 4.7k pull-up to 3.3v.
Pin 2 is "No connect".
Pin Number Signal Description
2 AGGREGATE4_7_L Aggregate Cathode - Connector J5 Ports 0-3
1 +3.3V Aggregate Anode
Pin 1 on the MB to Pin 2 on the raid card pulls the LED_SCSI_N low to activite the LED.