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Curious... what do you base this deduction on? What specs or parts are you referring to?
Only on listening impressions. Some even very expensive DACs like the Meitner don't have galvanic isolation on their USB inputs, so in that case its obvious why the sound would be better from a converter that's isolated from the PC ground. The Anedio's input is just their converter card internally wired to the DAC's digital receiver - so it probably sounds the same as the U2 into the S/Pdif input and many of the other converters.
Others I don't know as much about.
The Calyx is supposed to sound significantly better via USB than the coax input, so presumably they did something right there.