PostBell we have two close friends with the same first name but different ethnic backgrounds.
DD use to say Uncle Mike and Pink Mike. Then I taught her how to say Uncle Mike and Mike LastName when she needed to differentiate.
She could cope with this age 3 - its not difficult.
Re your DS I don't think that was racist, just a statement of fact.
My DD, at aged 5 got accused of making a racist remark when she said a girl had a black face, and the girl got upset. When I got to the bottom of it DD was actually referring to the look on the girls face rather than the colour of her face and was mirroring a comment straight out of a school book she had been read. I felt sad that the girl got upset. DD did not understand at although I tried to explain. We just work towards many ways of identifying people without defaulting to colour - which in multicultural London where we live, usually isn't that helpful anyway.
DD's father is Brit/Caribbean, I'm Caucasian. Not that it makes any difference.
DD's father and his family proudly identify as Black. I've sadly been subject to more racist comments from them than I would have thought possible. They usually won't even take on board that what they say/do is racist - or if they do they feel fully justified in it and it's OK for them to say because they are black
I don't let their ignorance bother me and I just try my best to bring up my DC in a world full of equal people, or many colours, physicalities, religions and backgrounds where everyone matters and everyone is important.