That is actually fairly simple: The machines DO grow the humans out there in the real world (please, don’t get into the matrix-within-the-matrix now, thank you for your corporation). How we look on a basic level is a question of genetics. The machines can just read the genetic code, program that into the pod-humans digital self… and voila. “He has his father’s eyes.”
Which is why Neo does look like Mr. Anderson. And vice versa.