In a September 15th research report published by Deutsche Bank Group, Takashi Oya and Kazu Ejiri suggest that Microsoft's decision to offer just one Xbox 360 SKU in Japan may be a result of lower-than-expected production output of Xbox 360 units.
They write, "We believe Microsoft wants to offer the scaled-down version but may be looking to control sales because of the possibility of not being able to meet initial demand." They go on to note that they believe that Microsoft will eventually sell the scaled-down Xbox 360 package without the hard drive and extra accessories once the company is able to rustle up enough of the consoles.
This may also explain why Japanese consumers are getting the full-blown Xbox 360 package for about $50 less than US consumers are paying for the same bundle. Since Microsoft isn't offering the scaled-down package in Japan, they had to give up some ground on price to hit their sales projections.