My name is Elias Gwinn...I'm an engineer from Benchmark. I can shed light on the topic of USB performance.
In all regards, the performance of the USB input is equivalent to the other digital inputs. This can be, and has been easily demonstrated with listening tests and/or test-bench measurements.
The Stereophile review that you referred to affirms this, but they also talked about a signal drop out below -60 dBFS. In John's review, he found that the DAC1 USB will mute when a single-tone sinewave (with TPDF dither) drops below -60 dBFS. This signal-mute is intentional - a mute function that prevents the typical 'clicks' and 'pops' from USB. It does not occur when music is being played.
The reason it occurred with this test tone, but would not happen with real music, is because it will only occur with a single-frequency sine tone (which is never the case with real music).
Also, almost no music is mastered with TPDF dither. Almost all music is mastered with 'noise-shaped dither', which will not activate the mute function.
Also, it only occurs below -60dBFS, which means the only sound that would ever be muted with that version of the DAC1 USB is the end of a fade-out of a single-tone sinewave dithered with TPDF!!
We have since adjusted the sensitivity of the mute function, such that even this unusual test-signal won't trigger the mute function.
If you have any more questions, feel free to ask...