The rods were just used to get in the way of amaterasu.
I don't think amaterasu is really meant for piercing, more like spreading on impact, just like the magatamas did on the zetsus. Since they spread on impact like normal fire does, of course they would spread once they hit the rods instead of piercing it. It did the same thing with the Rasenshuriken as Macho stated.
As for it not being able to burn chakra, it burned Bee which is made out of Chakra, and it also burned Rasenshuriken which is literally a ball of chakra surrounded by wind.