The funny layouts were also driven by copy protection methods. The methods took advantage of physical properties of the disk and read circuit that the processor couldn't see but a duplication system could.
The work by 4am and others was driven by the desire to preserve these works without needing to break the physical copy protection to do it.
The real annoying ones were the read the sectors in a block starting at 0 and going up you get one set of data. But if you run it backwards or do a deliberate seek you get a different set of data. Because of the interface or drive used or the firmware on that drive like you said. Starforce also used a variant of that. The super annoying ones are the ones that played with the ECC bits too or like the PS1 having a special wobble track. The laserdisc ones I am a bit excited for. They are getting some really nice images out of them vs copying it off the board in some random place or worse out of the svideo/RCA connector. Unlike the apple stuff they are having to resort to multi image copies to get an average of 'good' because of scratches or poor SNR out of some pickups. The apple ones can filter it to a point as you know you are supposed to get 8 bit chars out of it. With LD not so much though. Seeing the diff copy protections is kind of cool too like the ones where they put a special sector out of reach for normal firmware but they would re-write it on the fly and force the drive to read it. Think there were a few of those on the c64.
The work by 4am and others was driven by the desire to preserve these works without needing to break the physical copy protection to do it.