The part about tire fires producing "horrific incapacitating smoke" seemed a bit odd to me --- the landing gear are located outside the pressurised part of the fuselage.
An under-inflated tyre caught fire during take-off, the plane took off unaware of the fire, when the landing gear was retracted the fire spread burning through electrical and hydraulic lines.
A fire "outside of the pressurised part of the fuselage" doesn't mean the same didn't happen here.
...but that seems unlikely too, because I imagine the 777 has backup systems that would alert pilots in case a system as critical as the fire detection equipment in the wheel assembly was not responding.
I'm not saying the fire scenario is impossible; I'm still erring on the side of this being a tragic systems failure, and not a malicious act. I just think it might be entirely unlike anything we've seen in the past.