Data coverage has, perhaps, the biggest influence. NASA GISTEMP has the most comprehensive coverage, with measurements over 99 per cent of the globe. By contrast, JMA covers just 85 per cent of the globe, with particularly poor data in the poles, Africa and Asia.
This wouldn’t be a issue if the world was warming at the same rate everywhere. But data suggests the Arctic, for example, is warming more than twice as fast as the global average.
It’s reasonable then that a missing Arctic could lead to a global temperature that’s lower than in the real world. Indeed, updates to an old version of the temperature record (HadCRUT3) to include better Arctic data saw northern hemisphere temperatures rise by 0.1 degrees Celsius.