Hi Alex,
OK… I have compared the same song two ways. A 24/96 audio file from a DVD-A from the OPPO to the BDA-3 connected via SPDIF and the same file ripped and stored on a NAS connected to the BDP-3 (with a Cat 8 RJ45 cable) and the BDP-3 to the BDA-3 connected with a AES/EBU Cable. To my ears, those two sounds exactly the same. In fact, the more I make comparisons, the more that I find that anything CD-Quality (16/44.1) or higher, played with different connections, sounds the same. A CD played from my CD transport and the same file stored on my NAS sounds exactly the same. I came to the conclusion that this is a good thing.
In the past, the main difference that I found was when playing DSD files VS their PCM versions. I think that the difference comes from the fact that the file must be fed to the BDA with the USB cable. To my ears, high frequencies was a little bit more audible which can be interesting at times, but I found this cause listening fatigue (just my opinion). In fact, I converted all my DSD files to PCM (flac) and I use the same cable for all files to feed the BDA-3 (the AES/EBU cable).
And now, I return to listening to music and not to the system

Francois