I'd prefer "Bypass" with a high-end DAC - there's no reason to pay a premium for such a DAC and then stick it upstream of another DAC, which is what will happen with either Stereo or Upsample.

As for Pro Logic II, NEO:6, Stereo 5/7, or any other such mode, in my mind that doubly negates the point of a premium two-channel DAC. If you are going to use a mode like this with a digital source (CD, DVD, PC, ...), I'd just use a digital connection.