Thomas rejects the "idea" JonBenet was alive and clawing at the garrotte, because it doesn't fit with his "idea" of how Patsy allegedly staged the crime scene.

Steve Thomas' ideas are only ideas - his hypothesis as he calls it.
But whether JonBenet clawed at the garrotte can be proven as fact.

It's unfortunate that when faced with the truth he pretends to not understand the question, or gives a confusing answer. I understand the question and his answer very well.

He at some point recognized that if JonBenet was alive the crime wasn't staged by a distraught Patsy manipulating the cord around the dead body of JonBenet. Yet he refuses to accept that the FACTS do not support his "belief."