Hmm, I think I may have read that he hated that they couldn't build the full circular set, so had to plonk the Jockey dais between the 'piers' that project into the egg chamber. It was the compromise he hated, having to cut up the underside of the ship to form the corridors etc. This time around they planned it so they could redress sections of wall.
I'm not sure as to why it's less organic, but I'd assumed it was to make the ALIEN sets look like a denuded, ancient version of the ships in their pristine weapons facility state.