That's a good question. The basic Mustang interior panels and top stayed the same from 1994-2004.
I don't know if the change/split was an engeering alteration. Maybe styling of the exterior humps became more square for the 1999-2004 'New Edge' Mustang.
I've noticed generation split myself, but never really looked at why.
Small visual difference above the teardrop between the seats ( extra lip ). If I didn't mention it you wouldn't even know. The 94-98 cover will fit the 99-04 and vice versa. I wish I still had my 99-04 cover so I could take a picture side by side with my 94-98 for you so you could see.