I just wanted to say two things:
First, I didn't get too much of anti-athiest vibe from this book (have yet to see the movie, but what Bob described of the plot/twist/message sounds about the same). I got the impression that when Pi tells the darker story of his troubles, he is actively acknowledging that reality is not rosy or beautiful or any of that. There is no God. He just prefers to tell himself different stories so that he feels better, so that he can go on living his life without curling into a fetal position and giving up. So I guess I feel the "God doesn't exist, but pretending he does makes me feel better" doesn't come off as a purely anti-athiestic argument. Pi just had two choices, and he chose the brighter, fake one.
Secondly, I find it hard to believe the "quirkyness" of Pi could really be that obnoxious. In the book he's just a man who lost his entire family and spent hundreds of days adrift, near-death, who is struggling to cope. I know the "one friend" you're talking about, but Pi never came off that way. Of course everything in his life has a story behind it: if the dark version of his story is really true, he had to go through a LOT. So much so that the only way for him to keep on living is to give everything some form of meaning. I mean, what is more likely to kill your soul than losing your family in the most meaningless/arbitrary (storm at sea) and horrifying (cannabalism, watching as other people tear each other apart) way possible, while getting turned into a monster yourself.
So I guess I just saw the "giving everything a story" aspect of his personality as him resorting to extreme coping measures. During that voyage he was given insight into how truly empty, dark, and horrible life can be. How tragedy happens for no reason, and nothing can stop it. How do you live, when you know in your heart that's how the world is? I'm not talking minor cynicism here: true nihilism. The only way for him to come back from that was to paint a rosy picture of the universe and try to believe in it as strongly as he can, and he assigns EVERYTHING meaning to cope with the fact that nothing has meaning. This is not because he's "so calculatedly quirky." It's because he is an absolutely shattered man who can only exist in a dream world now.
Besides, MovieBob's opinions are 95% intelligent, interesting, and well-executed discussion, with 5% petty rage. Some of the "quirky" rage seemed petty here. Yes the tiger is named Richard Parker, so what? People like to give their pets goofy names, it makes them laugh. Etc.
I mean, I don't know how the tone of the movie's narration differed from Pi's narration in the books, I just heard more "CrankyBob" than "MovieBob" in the "quirky" tract.
Edit: Sidenote: Is it really necessary to always perceive a character's, even a protagonist's life philosophy as some kind of attempt to persuade other people to his/her way of life? There are some character choices/philosophies that are indeed an author's attempt to persuade the world to their way of thinking, but with a lot of characters they are JUST CHARACTERS. They're people, and they have opinions, and since the story is about that character we are likely to hear their opinion. This does not necessarily mean the author is trying to convert you. I always took all of Pi's statements and philosophies as JUST PI'S OPINION, and HIS PERSONAL METHOD OF COPING WITH LIFE. I never thought of it as a persuasive essay. Just a fictional guy talking about his experiences and opinions.
Of course, there is the whole "I will make you believe in God" line, but that to me still just feels like Pi talking to the interviewer, not the author talking to the audience. Maybe that's just me though.