More testosterone during the growth phase. So in theory, if one is leading a life that produces more or less testosterone, then they could be different.

maybe one had undersized tighty whiteys and the other had boxers.

You gotta get the right kit. Ever grown crystals?

Good question. For serious answers, try asking here https://lemmy.world/c/askscience or other similar communities.

On my part, I can vaguely extract some theories from memory.

One suggests some kind of insufficiency or excess during the growth phase can result in abnormal size of one or more organs, whether larger or smaller and usually accompanied by circulatory problems.

Another suggests it a remnant of evolution, whether specific to a type of environment or early societal development.

Of course, there's also the chemical imbalance issue caused by unchecked industrial exploitation and pollution that causes the entire biological chain to mutate uncontrollably.

But at their base, it's usually hormones that are directed in some way by something either to grow or to stunt.

Estrogen/testosterone balance probably. There are certain dietary factors that can change this. Tofu for instance has a chemical pretty analogous to estrogen, hence the term “soy boy”