That is because there are two schools, one says ok for bare metal, the other wants a sealed surface to bond to.
The logic is that filler acts like a sponge for moisture and will rust under the filler and bubble.
I have done it both ways, but currently am using epoxy primer on bare metal,(not etching) and then filler on top. It seems to work well, but truthfully I wont know for 10+ years how it really holds up..