Modern copy protection techniques are often based on this same principle. For example, the GameCube and Wii do a very similar thing. Since they use optical media, that doesn't have tracks but instead a single spiral groove, what they do is use a laser to burn little scratches into the disc (which you can see against a light). After mastering and lasering, the disc is checked to see what sectors the marks damaged. Error correction ensures the data is undamaged, but the drive can find these drop-outs. Then a table containing the sector locations is encoded and burned with the same laser into the "burst cut area", effectively a standard barcode format in the inner ring of the disc (this part is standard, many normal drives can read BCAs).
This all works because the specific angular position of any given sector is unpredictable during optical disc mastering. The groove is continuous, and never lines up in exactly the same way. So, just like the floppy trick, this is "fingerprinting" the natural variation in write speeds of different disc mastering/burning systems. This scheme is undefeatable using off the shelf burners, but one trick that Datel used to master compatible unofficial discs is to rip the encrypted BCA table off of a real game (so they didn't have to crack the encryption, though that was possible later since it's symnetric) and, instead of burning marks into the disc, just turning off the mastering laser writing the disc track at the exact same points in each track. Those discs don't have any holes, but they have a pattern of sector damage that is indistinguishable to the drive (even though the angular positions no longer match), and they work. I believe the same trick should work with a lightly modified standard burner, if you can manage to find a way to burn the BCA (and you need other firmware patches for some other data-level changes to the disc, but those are easier).
Xbox (360 and One discs at least I believe) also do this IIRC, but instead of intentional damage the drive has the ability to compute angular relationships between sectors I believe, though I'm not familiar with the details of that scheme.