Well, this is the whole point of asking for the stains on the pillow to be tested, since they argue there's a possibility they belong to this second person. In which case, he would have left some pretty definitive DNA evidence.
I wonder though if this is just an additional argument to get the Court to agree to the testing. If the theory is they belong to Rudy, the Court could just say it's pointless testing them anyway, since it wouldn't absolve Amanda and Raffaele. Whereas if the defence argue they might belong to a second person, that would change the whole theory of the crime, and so it would be important to test them.
From the defence's point of view, if the stains were tested and found to be Rudy's I think it would help their case, even if in theory it wouldn't absolve them. It would mean very strong additional evidence against Rudy in the bedroom, and would highlight the weak to non-existent evidence there against the other two.