Above the clouds,
Could it not be that the FGP was set to fly TRK and not HDG
TRK is still magnetic in this context so still subject to the large change in magnetic variation over the course of the flight.
The only way TRK could provide a straight track over this long distance would be if the HDG REF button, a guarded switch, was pushed. The MCP HDG lateral modes would then become referenced to True North.
If that was the case then the same problems of implied technical knowledge and intent rear their heads.