Same reason why the story for Empire Strikes Back came from George Lucas, but the script was written by Lawrence Kasdan?
I would think Moore and Braga had more to do than just pitch the story, though. Even if Robert Towne wrote the script, giving Towne a plot, a framework, characters to use, ideas to process, etc, is all part of the story, something Moore and Braga did
I'm pretty sure that Moore and Braga have mentioned before how their story was essentially gutted and the finished film bears little resemblance to what they originally conceived and wrote.
EDIT: Found this interview with IGN
So, the retarded motorcycle chase (with a bike that mysteriously changes wheels) and the final fight scene weren't their work.IGNFF: And what percentage of the film adhered to the work you did?
MOORE: The first two acts are essentially the structure that we came up with and the story we came up with. The third act was done by Robert Towne, or whoever, so it's a different ending. The initial structure of scenes is our construction, but I don't think any of the dialogue survived. The credit reads "Story By" Brannon and I and "Screenplay By" Robert Towne, and I think that's fair. That's a fair assessment of who did what.
"Gutted" sounds different than the quote you referenced, though. For one thing, Moore up there says they came up with the scene structure (and therefore the outline) was there with two acts. That's still much more than simply pitching a story.
Even a first draft of a script by itself is a daunting task, and it sounds as if even if they didn't write the final draft, they did write something that was later deconstructed and built upon. Hence, they still wrote.
Also, even if the motorcycle chase and final fight wasn't their work, that still means the two-thirds majority of the film, even if in outline form, was their idea. So there's more to the story credit than just mere pitching.