Well, yeah it does if the DAC processes one input better than another. And that’s really at the heart of my question.
No, you are wrong, it doesn't matter how well each input processes their independent signals they all have to go through the same OP amp output and to your power or pre amp. Therefore you should concentrate on matching your DAC output cables to whatever is receiving them.
Regarding AES/EBU most likely you will get better sound, the main advantage of USB is higher transmission frequencies. So unless you have files above 192kHz use the AES/EBU.