"Well, good for him"
I think it was a really nice touch that the director came up with.
SO, anyway, the whole end part of the movie focused on Arthur Allen as the prime suspect as in real life he is still the main suspect, but this particular movie implies someone else to be Zodiac.
It's Bawart. Take a look at the innocent camera work around him, while subtly emphasizing on him. And when Graysmith runs out of the police station, Bawart says "Well, good for him" replying to Mulanax' remark.