As cool as Batman is, there’s always something a little bothersome about people who argue that he’s just an everyday human who works very, very hard to do the things he’s able to do. His powers of deduction disappearing the moment people look away definitely seem like powers from time to time, and it stands to reason that Waller might honestly think that he’s able to do all of those things because of a meta-gene. She knows that Batman is Bruce Wayne, but she doesn’t necessarily know everything about Bruce’s biology.

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Regardless of what Waller does or doesn’t know, we can say with confidence that, for the time being, Batman is still a regular flatscan.