To rub salt in the wound for Loktar, the title isn't correct anyway.
I don't think they really explained it clearly enough in the episode, but The Flesh at the acid factory were some of the earliest of their kind. They were the forerunners of the type of Flesh that FleshAmy was, but coming from further in the future than them, her programming or design or whatever you want to call it, was more advanced, and instead of being a sentient copy, it was more like Amy's real consciousness was possessing the Flesh body. By destroying FleshAmy the Doc was releasing her consciousness back into her real body. "You haven't been here for a very long time." The Flesh body didn't have any sentience or consciousness of its own, as I understand it.
Must admit I'm not clear on what the Doctor's reasoning was for going to see the Flesh at their conception, though. If it was a test to see if the Flesh copies were inherently evil, then that's irrelevant since FleshAmy was created by bad guys from a future time who could've done anything with the design. And if it was a test to see how real Amy was, then I'm not sure how the trip to the factory really helped answer that question, since a Flesh copy would've responded in the same way she did anyway.