We can all speculate endlessly. A couple of things which I believe are, or at least could be, significant.
(1) The F/O was on his last training flight to type, and
(2) the opportunity existed for one pilot to lock the other out of the cockpit.
If either pilot left the cockpit and the other did lock the cockpit door it would have been a simple
matter for the lone pilot in the cockpit to don his oxy mask and depressurise the aircraft. Time
of useful consciousness, for those outside the cockpit without access to pressure breathing equipment,
would have been minimal leaving the handling pilot to disable the transponder and ACARS.
Of the two pilots it is reasonable to suspect the PIC would have the knowledge to do so. Why the
autopilot would have been disengaged, and for how long, is anyone's guess.
Whilst we may never find the answer my money would be on a deliberate act by one of the crew.