I wasn't in the Indie hall, so I can't speak to that. But to my knowledge, the ordering was done by Anderson's, not B&N, and they did order and stock Amazon Publishing titles and place those authors (or some of them, at least?) in the grand ballroom.

The announcer repeatedly exhorted attendees to go check out the NYT best sellers and other authors in the Indie room across the hall from the grand ballroom. I heard that announcement several times an hour in the grand ballroom during the signings. However, given that that exhortation was necessary, I can only imagine how incredibly frustrating it was for those authors to be set apart in that way. It wasn't just indie authors, either, but many who had e-first publications through small or large traditional publishers.

I think what mattered in terms of room placement was whether Anderson's could/would order the books for the show, and one of the deciding factors for them was the distributors' return policy. I wasn't at all privy to other deciding factors, however. Just an observer of how it went down at the event.