As I read it  the judge's  reasoning is based on Lee's deposition statements that he presented the artists with the plots or at least a plot framework either written or oral. In his deposition Lee says he created every key concept, and presented them to the artists to draw. The judge doesn't question Lee's testimony at all, because there is no one who can contradict it who has first hand knowledge.
As the judge said Marvel's case "stands or falls" on Lee's testimony.