The auteur theory itself is highly suspect when it comes to cinema for this very reason, at least as far as attributing every element to the director. It's more philosophical than literal.

I don't think the studio ever really had any say in his films though. They certainly didn't with THX and Graffiti, which was part of the reason they wanted to abandon the finished products, and thank god they didn't on Star Wars either, even though they tried quite hard. The collaborative success for early Lucas mainly came from the producer-writer-director-actor input, rather than studio.