What it says is, if someone's born without a penis, survives without it, reproduces and multiplies, a human penisless specy is created and you'd getanother stage of human evolution. Cutting off skin does not alter genes so the skin would not disappear, neither would the condition be inherited. Those who are quick to dismiss it, I find are totally ignorant of the subject. It has been observed to happen in many populations of species such as amongst populations of birds and fish.
Parents often tend to inherit their parents characteristics.
As to the Scientific content of the Qur'aan, it is how you interpret it. Some of them walk on their bellies, some walk on two legs, and some walk on four. Allah creates whatever He wills. Allah is Omnipotent. One interpretation could mean that life originated in the primordial soup of long vanished seas, or it could be referring to the high water content of our bodies.