A lot of Japanese companies are -blind- or -phobic- to the possibilities of the 360 unless a western publisher forces them to acknowledge its existence. Last month's Famtisuu 360 (single platform version of the main magazine) had a big cover: "THE ROAD TO 1,000,000 UNITS." Like it has finally accomplished something by hitting a million units. Thing is, the stretch from 950,000 to 1,000,000 has taken something like half a year. It's dead here, and the few fans it has here are just as baffled as you are as to why it will not sell.
Anyway, if ATLUS ignores the 360 in favor of PS3 exclusivity with no monetary compensation from Sony for it, they're simply following the "common sense" of the majority in the Japanese dev industry. Also, with the economic downturn, making games which may-or-may-not be sold overseas for a system that has no discernible domestic presence is also flying in the face of common sense. This ignores the fact that preparing / developing in a way which allows for addressing a broader audience overseas is a stronger means of ameliorating risk than trying to retrofit that stuff in after the game is finished for the 5 people who'll play it here in Japan.