If you read the Liverpool Echo live updates it says that Justice Yip said its perfectly normal for defendants to spend time with their lawyers and not be present in court, and not to read anything into him missing the pathologist part.
Also, maybe I'm in the minority, but I almost feel a little sorry for Y. I think he is niave, socially incompetent, desperate to please, gullible etc... his explanations seem quite reasonable and he is very honest. He knows he's been an idiot believing that X was just fantasising and I think he defends that quite well.
What will be interesting will be his explanation when they present him with the fact he DID take the knife that killed Brianna after all. That entirely changes the picture and in all likelihood will be his downfall