I don't have a PhD, but my understanding of the basics is this:

All people start out developing as female in the womb before a certain point where a large dose of testosterone caused (usually) by the Y chromosome activating (basically the only time in life that it does apart from starting puberty AFAIK) causes the proto-labia and vagina to push outwards and form the ball sack and enlarging the clitoris and urethra into what we know of as the penis. This is why you can see that line down the middle of your ball sack; that's where your labia fused together. It's also why the tissue that makes up your ball sack is biologically identical to the tissue that makes up the inside of the vagina. It's an outie vs. an innie.

There are many reasons why this wouldn't happen "correctly" since biology is more a wonder of things somehow working at all after evolution is done with them rather than a perfectly designed, well-oiled machine. Sometimes the Y chromosome simply doesn't activate, or it does, but the person has androgen insensitivity and so the testosterone doesn't do anything, or they develop as female but have testicles where their ovaries should be, rendering them infertile but otherwise a perfectly normal woman. Sometimes a person is XX, but they experienced a higher than normal amount of testosterone during development and developed male instead of female.

And that's before you get into the issue of intersex people, who are often surgically altered as babies when they're born by the doctor to match with the genitalia that the doctor thinks should be the "correct" one. In a number of places, the doctors don't have to ask permission or even tell the parents after.

Also, your definition of cis male is slightly off. "Cis" is the opposite Latin prefix of "trans," meaning a non-changing/stable state of being, and in this case it's used to mean that one's gender identity matches up with the one that you were given at birth. It ultimately has nothing to do with what genitalia you have, and it's simply an identification saying that your sense of gender matches up with the sex that the doctor declared and that you therefore aren't trans. It's an after the fact solution to the question of what to call people who aren't trans and comes from the use of trans to identify somebody who transitions from one gender to another.