Around 1919 was indeed also the time of ripper Stefan, however Klaus and Rebekah didn’t run into him until they arrived in Chicago, where they then spent some time together (without Elijah, who stayed in New Orleans to hold off Mikael). The events you’re talking about from 3x03 presumably took place around 1922 in Chicago, since Rebekah stated in 1x01 to Elijah that “not three years [after they left New Orleans] [Klaus] stuck a silver dagger in my chest and put me in a coffin for ninety years”.
So they didn’t actually leave out the Stefan storyline, it just happened later, after Klaus and Rebekah were already on the run from Mikael. Hope that helps clear things up. :)