I have a color deficiency. I took the old-school light gun test at a local airport after I had a student pilot cert. that had a night limitation and passed with no problem. After that I was issued a "Statement of Demonstrated Ability" or SODA. It was a one time deal that I never have to repeat and I skip the isochromatic plates every time I get a physical.
I hold a 1st class medical with NO LIMITATIONS. As I understand it they no longer issue SODAs and I think you have to take the Farnsworth Lantern Test, which was only one of the choices I had back then(10 years ago). I may have that wrong. They issue some other piece of paper now that has another name.
You'll find that it's a well-traveled path but I would have him go ahead and get the Student Pilot Cert. so he can get the folks at the FSDO to actually pay attention to him and get the thing taken care of.
Now all of this is predicated on the assumption that your son can see the colors well enough. As far as airlines hiring him.....if he has a 1st class med. with no limits there should be no problem. Even with a company physical. But find an AME that has experience with this sort of thing(waivers, SODAs, etc) and stick with him. I like seeing "NO LIMITATIONS" in that box that says Limitations.