I don't think there's anything really special about Nero. As far as I know, BIN/CUE is the most popular format for PSX.
As for the PSX copy protection, I've seen a number of theories (some of which are clearly complete BS, such as "the PSX checks to see if the disc is black"), but I believe the best explanation is that the boot protection is the presence of non-standard (I've heard all-zero) data in the EDC/ECC areas (the ones defined by Red Book / IEC 908, not the ones in Yellow Book / ECMA 130). As far as I've been able to tell based on reading final drafts of the SCSI MMC standards (the actual ratified ones cost money...), there is no command to read or write these areas. They are apparently handled by the burner's processor or possibly an ASIC, which probably results in standard EDC/ECC encoding on all discs.