@farmerman,
The 2011 cockpit fire at Egyptian Air started in the cockpit o2 system might come into play, this is a massively mismanaged airline, the retrofit might not have been done right.
My main wonder is if the pilot could mumble to a passing aircraft as they ran out of breath why couldn't they contact ground controllers? Second is assuming compartment had a functioning o2 system why no cell phone activity? Too much smoke?
But the cockpit fire idea has problems too, because while it might have knocked out the transponder why was another data relay system not even in the cockpit also not working? Why as auto-pilot still working? Why couldnt the pilots get the fire under control? Even if the cockpit 02 system was down they could run and get a cabin crew tank.
Fire with the lithum batteries in cargo, maybe knocking out the o2 system AND all communications? Maybe, but no time to radio before discovered and it got that bad?