I think Batman has mostly pieced it together after the fact. Yes, he was there when the Red Hood fell into a vat of acid, but I don't believe he saw the Joker emerge. At the time, I believe his reaction was akin to "eh, can't save 'em all."
If you're asking whether or not that origin for the Joker is canon, it is. At least, in the New 52 it is. Which is kinda' what matters right now.
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