I too wish I knew the reason for many of the seemingly arbitrary values used by the code. There seem to be many...
Perhaps this particular issue has something to do with the physics of heat dissipation from conductors and equipment. A full load at less than 3 hours must not have the time needed to develop the heat the could possibly damage the insulation or termination if the conductors are sized correctly, whereas full loads of over three hours tend to get to temperatures that exceed the rating of a properly sized conductor without the 25% increase.
