2) In my system (through my ears and with my brain) ape sounds better than flac and almost indistinguishable compared to wav: I know, this is a highly controversial debate...
Impossible.
Both are lossless and are exactly the same as uncompressed wave. There is no debate possible on lossless formats.
Impossible?
It is funny how even an accurate choice of words to indicate a subjective sensation/opinion doesn't help to prevent to be attacked or, worse, be derided.
I think that, while identical at bit level, flac, ape, and wav can sound different: is it an absolute truth? No, it is just my opinion.
Have you ever thought that, when a computer outputs a timing dependent signal such as S/PDIF, the computer itself becomes part of the analog processing?
S/PDIF is usually clocked by an oscillator inside the motherboard or the sound card, goes through several logic devices (CMOS gates) before being presented
to the output connector and these circuits get power from the computer's PSU, the same that supplies power to the CPU.
CPU cycles, number of operations, and temporal distribution of these operations are largely determined by OS, programs running, and
type of audio files to be decoded.
The CPU induces perturbations on PC's power supply in form of voltage variations and variable magnetic fields and these perturbations are correlated to CPU activity that doesn't
mean necessarily CPU load %. Even power save mechanisms can influence power supply.
Now, no oscillator and CMOS logic is immune from disturbances on its power supply or EMI induced noises (even mechanical/microphonic as crystal oscillators are based on piezo devices):
those perturbations are reflected on the phase noise of the oscillator and therefore on the jitter present at the S/PDIF output.
Asynchronous USB DAC might be a different story unless the receiver side is not powered from the USB cable and thus from the PC power supply.
Any PC is different in terms of CPU model, PSU, mother board, memory brand, hard drive/s, wiring layout, etc. : with my CDs, my PC coupled with my DAC, my preamp,
my power amp, my listening room, my ears and last but not least my brain, ape sounds better than flac!