Even if Bay hadn't made the comment he did it would still have come out that they were changing the turtles origin.
If anything it would have been worse because at least with Bay's throwaway comment a lot of people thought he'd misspoke. Liebesman even tried to conflate it with the original comic book TCRI origin; at least some people bought it. If it had come out later then no one would have believed their attempt at damage control and it would likely have been too late to change it.
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