First, a caveat. I am by no means an expert on digital audio transfer protocols. At Charlie's we were auditioning SPDIF cables, not USB. I definitely heard a significant difference in the cables but have no idea of the mechanism that caused those differences.
There is a difference in the mechanisms of data transfer with SPDIF and USB. As I understand, in SPDIF the clock signal is carried internally on the signal in the form of a biphase mark code. In USB the data is transferred with three methods, isochronous, interrupt and control. The audio data uses the isochronous method, interrupt handles actions such as muting, and control is for operations such as device capability inquiries. USB does not rely on an imbedded clock in the data stream.
Beyond that I cannot comment on differences in the two but the general consensus is that USB results in more controlled transfers. Don't quote me on that. If that is true it MAY be that the SPDIF (or AES/EBU which is essentially the same thing with different impedances and methods specified for the connections) is more sensitive to cables than USB. I don't know. Currently all my digital audio travels aver USB connections. If you want to get into the weeds, here are two references you might find interesting.
https://en.wikipedia.org/wiki/Different ... r_encodinghttps://www.xmos.com/developer/download ... 1.0%29.pdf