IIRC from that time, those CD-ROMs contained two tracks, one formatted with ISO 9660 and another with HFS+. Windows didn't come with HFS+ drivers so it ignored it, and probably MacOS prioritized mounting the HFS+ track.
I've seen some where the combined file size exposed on each track would be larger than a CD could hold, so there had to be something more going on. StarCraft and Brood War come to mind with the large StarDat.mpq / BrooDat.mpq files.
Oh, StarDat.mpq, brings back memories. That was one of the major reasons I'm in this industry now - the file itself is a "virtual file system" (MOPAQ, with MO being IIRC the authors' initials) file with some CRC and obfuscation. As a kid, I was hell-bent on learning how it works, writing code to decode and encode it, and then use it in my own hobby projects. I learned a lot of concepts from that little rabbit hole. Hell, the way StarDat.mpq, BrooDat.mpq, and Patch_something.mpq interacted, was what you'd call "overlay FS" today.
TL;DR ISO9660 provided an area to stuff type-tagged extension information for each directory entry.
In addition, first 32kB of iso9660 are unused, which allowed tricks like putting another filesystem metadata there.
By carefully arranging metadata on disk it was then possible to make essentially overlapping partitions, stuffing each filesystem metadata in area unused by the other, with files reusing the same space
