I'm afraid the certain piracy site is wrong. I have the first release boxed edition of Quake retail, version 1.01 CD, which I bought myself in 1996, and it does have pre-emphasis set. Here's EAC For that disk:
I'm fairly certain the pre-emphasis flag was set in error, but what I don't know is whether or not the audio was also de-emphasised in error as well, so what is the correct version - de-emphasised or not? I'm currently leaning towards de-emphasis being necessary, based on listening to the results. But I'd prefer to come up with a logically tight reasoning for what would be right.
FWIW, back in the 90s CD-audio was been decoded by the CD-ROM drive in the computer and analogue audio data passed to the sound card over a dedicated cable. So the CD-ROM drive itself interpreted the pre-emph subcode and applied the de-emphasis curve.
@BenAkenobi , one possibility is your digipak is a later, fixed version. Would you be prepared to share a FLAC/EAC rip of that CD with me for testing purposes? I can reciprocate with a rip from mine. If so let's take it to PM.