Brett,
The phases would be similar because they are on the same card. However, your impedance for the M-Series device is going to be different than that of the FGEN and Digitizer. You would have to take into account the impedance of the input as well as the output and try to match those for your application. The details on the impedance of the PXI-6120 can be found here.
Aaron W.
National Instruments
CLA, CTA and CPI
