Short answer: Who knows? But leaving aside my views on the veracity of independent (i.e. not published by the major dailies) weeklies, including the authenticity of their sources, the article boils down to two points:
1) The Hatoyama administration is dithering over Futenma because the DPJ fears the SDP.1) is only partly true. SDP’s internal dynamics—the election manifesto, the leftish elements, its unanimously anti-military base Okinawa contingent, Hatoyma’s personality, Okada’s personal attachment to the Kadena option—have at least as much to do with the confusion as the SDP’s position does. To look at it from another angle, I don’t think this is a coalition breaker for the DPJ.
2) The two sides got into a diplomatic pissing match because Obama administration is pissed off at the Hatoyama administration for dithering over Futenma.
As for 2), this is the first time that I heard speculation that Obama had delayed his departure one day to express his displeasure. I’m sure there has been some speculation about Hatoyama’s motives. Me? I think a tit-for-tat would not be conducive to a satisfactory resolution of the problem. But then, maybe none of the advisors on either side is smarter than your average kindergartener.
I can think of perfectly legitimate reasons for Obama not leaving Washington immediately after a top-priority, inconclusive NIC session with no easy conclusions, leaving most of the principals behind to wrestle with the question in his absence. (Now that would have been Kobe beef for the right-wing media/blogs.) Of course anything is pure speculation unless one has access to his full itinerary—which I assume that the Japanese writer is likewise not privy to.
As for Hatoyama, the reason given in Tokyo was that he left because he didn’t want to skip the APEC inaugural dinner. And what’s wrong with that? So he should have accommodated the last-minute changes in Obama’s itinerary by staying on for the last, ceremonial leg of Obama’s visit and given up engaging, as a newly-minted Japanese PM, in Asia-Pacific summitry in Singapore? What kind of message would that have sent to Japan’s neighbors, especially when he would be hosting next year’s APEC summit? The clincher in my view is our Emperor, who, from a ceremonial perspective, is better than a run-of-the-mill [head of state]. The Chinese authorities have been using their Hu-Wen tag team (and odd-couple Jiang-Zhu before that) to great logistical advantage; now, Moscow is putting Medvedev and Putin to the same task. True, the Emperor has no power—but does Dmitry?
Occam’s Razor, I think.
That said, if some people want to take a single tabloid article as gospel, that's their problem, not mine.