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Thanks for insight into the Basic Relations Treaty. As you point out, the situation could potentially provide slight problems in the future.
While the Korean decision to not go into arbitration with Japan may not necessarily be breaking any "rules" of this agreement, soudenjapan is correct in pointing out that doing so is at least against the spirit of the agreement. I think Koreans understand that they have choices that they need to make, despite how unfair it is. I think they will choose to take that risk (whatever that is) and not go into arbitration. If the shoe were on the other foot, the Japanese wouldn't either, of course.
This does happen on occasion, you know: The Americans completely broke away from the Anti-Ballistic Missile Treaty with the Russians. MAYBE the Americans will pay a price for this choice in the future, maybe not. Anyway, the decision the Koreans are making isn't anywhere near as severe as the ones the Americans made with the ABM Treaty.
One thing I disagree about soudenjapan's assertion is that "Japan promises to agree with the decision of a third party, whatever it is." Well, the Japanese can "promise" now, and change their minds later. Japan losing to the Koreans AND agreeing to follow the decision would be a major embarassment to any Japanese administration, so let's not kid ourselves. And I can't imagine certain interested parties in Japan would agree to such a loss. Maybe you believe in promises made by governments, soudenjapan, I don't. Promises are like a$$holes... I won't even go into the trust issues regarding the two countries and their past history, especially considering that Dokdo is a part of that contentious history.
It may not be pretty, but that's where it stands.