No. That cracking group would have known a priori the phone call was a pretense, because id was very unlikely to press distinct CDs. So they could focus on conventional cracking techniques.

Maybe have n versions of the CD (maybe 16, or 32), so there are n decryption keys. When the buyer recites the code over the phone, the program run by the salesperson can identify which key is used based on the number.

The hacker groups would be a little frustrated trying to find all of the different CDs.

A reminder that CD-ROMs are pressed from glass masters, not burned like CD-Rs. I wonder if anyone has tried something like this with burned discs, though.

Some sort of public key crypto scheme + including hard-to-change local device characteristics in the challenge.

You would need some sort of hardware serial number system for PCs and a whole security infrastructure to verify that the serial number being used for the unlock wasn't faked. Then you could do per-PC unlocks. I'm not aware of anything like that being widespread back in the Quake days, though these days every computing device you own probably has a unique ID burned into ROM somewhere.