I found that MCT QPD has dependence of the total output on the position of the spot. Since the QPD needs the supply and bias voltages from the sum/diff amp, I could not separate the problems of the QPD iteself and the sum/diff amplifier by the investigation on Tuesday. On Wednesday, I investigated a generic quad photodiode interface module D990692.
This is indeed sad. But, we can perhaps bypass all of this by just using the individual segment outputs. According to the circuit diagram and the c1iool0 .db file, we should be able to just do the math on the segments and ignore the VERT/HOR/SUM signals completely. In that case, we can just use high impedance for the sum/diff buffers as Koji says and not suffer from the calibration errors at all I think.