Well hold on, if he can measure the output of the toslink-fed signal versus USB-fed signal, then he can be sure. It might be worrying for new buyers if this problem still persists even on certain 2004+ boards. I was also worried about this before I ordered my E30+L30 combo, still haven't recieved them so can't check atm.
What I'd do is connect the dac to the PC with both USB and TOSLINK, then do the absolute polarity blind test. I'd make sure to hear it first correctly with USB, get something like 5/5, then just flip the switch to TOSLINK and try guessing the next one without re-listening to the original or inverted phase. If suddenly you start getting all of them wrong, it's likely the phase is reversed for TOSLINK. If you keep doing them perfect, then the phase is the same with USB and TOSLINK.
What I always wondered is how they address the polarity issue with the driver for both pre-2004 and post-2004 boards. Did they revise only COAX/TOSLINK out in hardware, and then kept the phase fix only in software for USB? If they revised the board completely then the driver would re-invert the phase for 2004+ units, no?