it is clear from reading this document that investigators are working on the idea that the crew was unconscious
No, it isn't clear at all.
Being on autopilot says absolutely nothing about the state of the crew. A perfectly alert crew would also spend most of this trip on autopilot.
Also the document clearly states in bold type some of the assumptions were only made for the purpose of assisting in the search and may have nothing to do with the actual causes of the accident (page 35). They emphasize they are not accident investigation committee and shouldn't be confused with one.