The anime is based on the first four novels. There's a year gap between the fourth novel (Baccano! 1932: The Drug and the Dominoes), and the sixth and seventh novels (Baccano! 1933: The Slash). (Novel 5 takes place in 2001.)
There's a year's worth of events that the novels gloss over - several character relationships have changed dramatically since we last saw them, and the novels cheerily leave that up to the reader's imagination.
The three bonus episodes tell a story that takes place during that gap, and connects most of the major dots, while also working in a few loose ends that didn't quite make it into the TV episodes. The TV ending was extremely satisfying - it was the end of each novel's storyline, after all - but the bonus episodes both provide additional closure while simultaneously setting up the next storyline, should they ever make a sequel.
Definitely not filler - there is an anime original storyline that connects all those pieces together, but I imagine Narita was heavily involved with that. If he wasn't, than that's because the anime staff understand his work perfectly.