This isn't foolproof, some games don't like the change. Pinball Illusions, Pinball Fantasies, Fire & Ice and Skidmarks 2 all work fine. So long as the CUE file has CD32 at the end of the filename they boot and auto setup the CD32 pad.
Seek and Destroy and Alien Breed 3D will not boot in this format, instead they bring up the 'Cats Eyes' BIOS screen. I'm totally lost as to why as the other four CD32 games work fine so the BIOS clearly cannot be the issue.