Thinking about it, I went to watch Edinburgh rugby a few times when I lived there. There was still actually a fairly decent atmosphere in Murrayfield (capacity ~67000 IIRC) with a crowd of less than 3000. I think maybe poor atmosphere and poor attendance in a large stadium stem from the same root, and don't actually have a causal relationship with each other.
Edit: they tended only to open the few blocks either side of the half way in the west stand lower. Kept everyone nicely together, it still sounded noisy, and presumably kept the costs down.