This isn't limited to just Japan, its often the case that record companies and bands issue slightly different releases of the same album, dependant on country. So some countries might have a slightly different track listing and or some B-Sides or a couple of extra tracks.
This used to happen a lot between the US and the UK as record companies adjusted for differences in what was culturally acceptable in the two countries, doesn't happen as much any more.
Its also not limited to the content of records either, sometimes separate album artwork is created for an individual country.
Check out this Wiki article on "Are you Experienced" - Jimi Hendrix Experience to see what i mean:
As for releasing an album only for a particular market; this is based on how receptive the market is to the album, and is the same for any product regardless of whether its music or not. So the record company thought that the record would sell in Japan but not as much elsewhere, so they decided to spend their marketing budget only in Japan. They know that other people who want it can still use the internet :)
Virtuoso guitarists like Yngwie Malmsteen and Paul Gilbert, seem to do very well in Japan