I am not sure, but I have some theories (related to the playback system differences) that are involved (none of which are really original thoughts):
“If the bits are the same then either the transmissions of those bits or the conversion to analog are somehow suspect [different].” – Paul McGowan
“So, the question of which medium sounds better is really better asked—which retrieval and playback technology is on the current forefront of digital audio reproduction?” – Paul McGowan
“It isn’t the storage medium that matters. Rather it is the means by which we handle and process the data that determines how it sounds.” – Paul McGowan
CD/SACD player systems May be different/“noisier” than hard drives when it comes to the physical retrieval and transmission of the bits into the signal path leading to a DAC
Hard drive systems May be different/“noisier” than CD/SACD players when it comes to the physical retrieval and transmission of the bits into the signal path leading to a DAC
“The thing to learn here is that jitter is the #1 issue with digital and it can be minimized whether you are using a transport or playing ripped or downloaded files. They can both sound world-class with the same jitter when feeding a DAC that has no reclocking on the S/PDIF coax input. There is nothing magical about spooling files or spinning an optical disk. They both deliver the same data in the same way. The way to optimize SQ for digital is to attack the jitter.” – from this thread: CD Ripping: Sound Quality Comparisons Between File Playback & Optical Disc Playback | What's Best Audio and Video Forum. The Best High End Audio Forum on the planet!
This last bullet intrigues me and rings the most true (no pun intended), based on my limited reading.
It is my understanding that @tedsmith has focused on two priorities with his DAC designs and FPGA programing: 1. the virtual elimination of noise on the line, so to speak; and 2. minimization of jitter. In theory, the better the playback system is at minimizing general noise and noisy jitter, the better the result.
I have a hunch that, to date, my system is configured such that file playback is less noisy/jittery than disc playback.
I also found these linked videos referencing Ted Smith talks addressing jitter to be very informative – if not mostly beyond my technical understanding:
Why Jitter Matters
Jitter’s audible effects
Jitter and clocks
I have much more to learn, but I hope the above is at least helpful in prompting some further research and thought on your part.