The implication is different I would guess. As well as the large number of people that look at both words negatively, and also things never translate quite perfectly. You should know that.
Perhaps it's that nerd is typically associated with social inability, while otaku is a culture, so friends of the same obsessions gather together. It's like how Trekkies were considered weird for outsiders, but as a group they could find friends easily.
Or maybe, the universe is actually purple and none of this makes any sense or matters.