I reckon s3 is what we call the 40th anniversary model. It's a s2 with extra bits like badges and embroidery on the headrests and options for bodykit and steering wheel etc.
Not sure how you've broken the vins down, but certainly the 40th is 1998 only.
As far as real-world lingo goes, noone has ever said "series three" in regards to a GTST infront of me.