I don't think there's much doubt that it's the second story that's true, not the first, though it speaks to the power of the first story that we all want so very much to believe it.
I remember clearly thinking in the first chapters after the shipwreck - Really? A tiger, a zebra, a hyena, an orangutan and a boy, all in a ship's lifeboat? Really? But then when I became so engrossed in the story and Pi's description of the animals's behavior, I completely suspended my disbelief.
That Pi gives the tiger a human name - Richard Parker - is a big, big clue, but I chose to ignore it as I dove into the story.
On one level, it's a very successful piece of writing, because you ignore ALL the evidence that this not a realistic story because you want it to be true. The huge slap of disappointment and almost betrayal that I felt when I read the section with the interviews means the earlier sections were effective. But I still can't consider it entirely good storytelling, or being honest with the reader.
Under no circumstances should you EVER, EVER read the author's subsequent book, Beatrice and Virgil. Just don't, you've been warned.