Yeah, I have both the mainline manga as well as Shooting Star and when I do think about Bebop, I usually think more about the episodes than any story from the manga, even though they're not that bad.
Also, I get the feeling that the stories in the mainline manga were based on ideas for the show, but were scrapped for the episodes we got.
Fun fact: the magazines the two manga appeared in were shojo mags of all things.