So, it’s shown that there are enough redhead genes in the Fenton family to get a redhead. See:Jazz. But to get a redhead you need both blonde and redhead genes.
So, in this au Danny is a toe head. He’s basically a platinum blonde about until his sophomore year when he’s been doing this superhero thing for a while, and Phantom, in a strange twist of fate, actually has black hair. Until, suddenly his hair starts changing color.
It all happens rather quickly, actually. His hair becomes noticeably darker by winter break when he starts to notice he’s a dirty blonde rather than almost white like he used to be. On top of that, phantom’s hair seems to be going grey.
This goes on until by the end of high school Fenton and Phantom look the way we see them in the canon universe, with Fenton having practically black hair and Phantom having white hair.
The only person who makes the connection is Wes. Nobody believes him. Right before graduation Danny bleaches his hair just to piss him off. Still nobody makes the connection. Wes flat-out screams at graduation.