Frankly I don't think there will be much audible difference between bit-perfect 44.1KHz capture, converted to 48KHz to be BD/DVD compliant, Vs. analog capture (with a very good ADC) directly at 48KHz...
I think also that the analog tracks have very good quality - if japanese chose to put the japanese audio in the analog tracks instead of the PCM ones, *maybe* there were good reasons to do that!
I read somewhere, years ago, that the analog tracks could sound more "natural" than PCM ones, but this is "fuel" for a completely different thread...