My (admittedly limited) understanding of the case so far is that neither Uber nor the former Google employee dispute that the theft did in fact take place.
No, you're wrong. Uber doesn't know if Levandowski stole the documents or not. But they are saying it doesn't matter, that any stolen documents are between the individual and Google, because none of those documents made it into Uber's code base or designs, and none of Google's designs are in their current research Lidar, which was developed by an entirely different company that was bought before Levandowski even left Google.
Forgive my ignorance, but can Uber dispute that the theft did in fact take place if ther former Google employee isn't saying anything? Could they not be as ignorant as you or I?
They could be as ignorant, but the fact that they haven't forced their employee to disclose anything appears to the judge that they're trying to have their cake and eat it too.