the augmentations appear to be mechanical, similar to those of the unatco mechs, but this would mean that the metal would have to grow with the foetus, and metal cant grow. I think that mechanical augmentations would have been surgically implanted into a grown adult. similarly, the early nanotech augs would have been infused into the dentons once they reached adulthood.
also in deus ex, we learn that scientists had found it impossible to mix nanotechnology with metal. but versalife overcomes this barrier and they create the dragons tooth sword.
if you take all these facts, it seems most likely that the foetus is a new generation of augmented human, nanotech components are present from conception, and they build what is effectively a 'living metal' that grows with the body. this would combine all the strengths of mechanical augmentation with all those of nano augmentation