Possibly it's because the book is so much an intellectual puzzle box. Ruth Ozeki, married to Oliver Kellhammer and living on an island in BC, writes a story about Ruth and Oliver living on an island in BC: and that's just the first of the confusions between fiction and reality. As Pratchett says, it's all probably due to quantum: only in this case that seems to be literally the case. Possibly it's the engrossing semi-mystery of the main action- "MS Found in a Hello Kitty box". Certainly for uncritical reader me, there's the unexpected ways in which the two narratives echo each other. Schoolgirl Naoko is writing in 2001 and sees the fall of the twin towers; novelist Ruth is writing around 2012 on an island in BC, waiting for wreckage from the tsunami to reach the shore. (Wreckage does, but there's no proof it's from the tsunami-- 'too early, and anyway we're too far in to get much.') The destruction wrought by the tsunami and the Fukushima meltdown have the same resonances for Ruth as 9/11 and the Iraq war have for Naoko.
(Which actually makes me wonder about something. Somehow I don't recall equal concern or an equal number of articles about the 2004 tsunami that was far more devastating but lacked that basic nuclear factor. But even when they're not concerned with radioactive water, nobody is writing a Ghosts of the Tsunami article about Indonesia.)
All this plus Buddhist nuns. The Time Being was an interesting place to be; it's only now that I've come back to a Novemberish April in TO that it seems so odd. Some of that is indeed tsunami-connected: anything connected to March 2011 has the uneasy-making smell of that painful, unreal period. Compared with the impossibility of that month's events, the book's weird events are mundane. Of course ghosts come back at o-Bon, and of course you can talk to them. Several Japanese have told me so. Of course books change their text. I've experienced it myself. Thus I'm not sure if one should classify A Tale for the Time Being as fantasy or speculative fiction per se; but it's a bit outside the (dull) givens of mainstream novels, so perhaps I will.