I think your thought process is correct with regards to the I/O. From what I’ve read it seems that the MC looks for a reference- and whether that’s via an AES/SPDIF input or an individual BNC Word clock input (rear input connections) it would correlate to the selectors on the front panel. My assumption was that if you’re using USB for signal and clock reference none of the others would need to be selected. I don’t understand why it would want another timing source if only USB was used. I’m assuming you had the Mac and USB all connected with a source playing while setting up the MC3? My question to Mutec would be “why do I have to select other input references to have audio throughput when I’m using USB as a source”.
BUT- there might be something in all of this that means the MC3 is outputting something strange to your speakers DAC and/or signal network. Just my guess.