You seem to have missed the point that this is
not a criminal case, so the Fifth Amendment doesn't apply here. By pleading the fifth, he's not just declining to testify — he's claiming that the result of cooperating here would open him to a whole different criminal case.
In other words, nobody is saying that he has incriminated himself by pleading the fifth. But in Uber's civil case, he has created some very bad implications and greatly worsened their position, and it wouldn't be unreasonable for them to see him as a liability at this point. This is not a mere accusation by Waymo — his actions indicate that there's something going on here.