S3M is just a MODule in a different format, reflecting the hardware capabilities of the PC-bucket sound cards. It‘s a technical necessity since mechanically, the way this type of music is composed and played is tied to the hardware.
S3M could do a lot more than the old MOD format though. Mainly the support for more channels and instruments made a world of difference. It's the same basic principle, but creating a track was far less of a priority puzzle in Scream Tracker.