This reminds me a little of the opening of the book He, by John Connolly--which didn't make a lick of sense to begin with, but soon starts to justify itself, and eventually becomes an enjoyable, uniquely evocative read. In that case, it is clear the author had a plan: I will baffle them on the first page with by throwing the reader into the deep end of the pool, then slowly lead them to the shallows so they don't drown, but still remember that they are wet.
A few hundred pages into the book, I was trying to figure out whether I had gotten used to his unusual presentation, or whether Connolly had really slipped back into a mostly conventional (and completely effective) deep-perspective story-telling technique. I think the answer was a little of both.
Someone earlier commented about Brecht and the concept of alienation in theatre. I see that as forcing the reader/audience to be conscious of the medium (IE, words on a page, or people or stage, or images on a screen) in a way that artists mostly work hard to obscure. It's like they are saying, "Psst--remember, you are reading a book here. Just go with it." The idea, I think, is to give the part of their brain that processes and interprets art a sort of "hard-reset," clearing out previous expectations.
Forcing that kind of alienation can have a value, depending on what you're trying to achieve, but it also demands a certain amount of trust between reader/audience and artist. If you readers don't have any pre-existing reason to trust you (for example, they've never heard of you, or never seen and enjoyed any of your previous work) alienating them on page one/scene one is probably not a winning strategy. Save it for later, when you have built up some equity in your relationship.
Something more to consider: if you took a well-read Victorian and handed them a contemporary novel, written in the spare, fast-paced, and deep-perspective style that has achieved so much acceptance today, they would probably be quite alienated too by the first few pages. My point is, one's interpretation of art is heavily based on one's expectations. And, culturally, our expectations do change over time. For the most part, they broaden; as today, I can read a Victorian novel and enjoy it, but I can also read a contemporary novel and enjoy that too.
I confess I have not read any of Flanagan's works, so I can't say how much grace I would be willing to give him with an opening page like this. Since he's so well-regarded, I'd like to think I would give him a few pages to start pulling me back in, but it probably depends on the mood I'm in. Dave, since you've actually read this book, does he go in-and-out of this mode later on? By which I mean, shock opening, slow fade to conventional story-telling, interrupted by periodic moments of alienation to keep the reader from getting too comfortable? That works for me--assuming the conventional parts are sufficiently compelling that I'm willing to work hard to get through the occasional "meta" elements. At the end of the day though, there still has to be a good story and characters I can relate to. If you haven't got that, I don't rightly give a damn how many Booker Prizes you have on your mantle--I'll be putting your book down.