That is my point, the AES/EBU interface should not alter its behavior based on a setting that in theory only affects the USB interface. In my case, if I set the "Use native DSD on USB" to OFF, then I can play all sorts of DSD files using the AES/EBU interface, and if I turn the setting ON (Which in theory should not affect the AES interface) the opposite happens, I can play FLAC files, but no DSDs at all, not even DSD64.
This is likely because when you enable the native DSD signal that is what’s being sent to the AES/EBU as well and it cannot process that signal and so sends nothing or maybe it’s not even sent to AES/EBU at all — whatever, but when the native DSD is turned off the signal is “dumbed down” however it’s done which is why the AES/EBU connection can then handle it. What @audphile1 recommends makes total sense that if you’re not doing DSD use the AES/EBU connection as that is better for the reasons stated (OCXO clock) and when playing DSD use the native DSD signal through USB. Seems simple enough.