I suppose that's kind of why I'm confused. ISO files don't have CUEs do they?
For certain systems, ISO+separate audio tracks with CUE was the preferred format in older days, today this isn't as important because of increased bandwidths and space. I don't think separate audio tracks were really a thing with PS1 images when people started to share them on the web in the common places, I assumed there were technical reasons for it. Maybe it's just because lossless compressions(like FLAC) weren't really known or available.
ISOs with separate tracks are in some cases still necessary, e.g. I believe Final Burn Alpha's Neo Geo CD emulation only works with ISOs, not Bin/Cue files.