I'm not an expert, but I think it's like this . . . .
Saying "I said that I HAD been waiting . . . . etc." moves the sentence farther into the past. So you don't want to move 'he had arrived' even farther into the past, because the time relationship between you waiting for the bus and his arrival did not change.
Another example:
I was eating when a dog barked. changes to:
I said that I had been eating when a dog barked.
The overall sentence has changed, but the time relationship between EATING and the DOG BARKING has not changed. So, 'when a dog barked' does not change.
I've never thought about this before. Hopefully this makes sense.