Why was his skin colour picked as the differing factor between him and Senna? Isn't that racist? Is it racist? And if so, which part is racist? The part where you point out his race, or using Chocolate as "black"?

For the comedic effect of that nickname to work, Senna is related to his character, since he shares some things in common with Senna, or at least there seems to be a media narrative to it. And the adjective is about something inate that he can't control. This is to point out that he's Senna, except he's not because of that characteristic. You could argue that his skin colour was picked because it's the most obvious difference between him and Senna.

If they were opposite genders, would it be sexist to make a joke like this? Is it our cultural background that necessarily makes this racist? Or is it inherently racist? Or is it that it's racist because people who use/created the term wouldn't have made it if there wasn't a racist underlining in there?

I honestly don't know. Some people clearly find it offensive, I don't much care for what is or isn't offensive, but if the mods don't want people to get offended then I can't blame them for the ban, since some people clearly were offended by it.