I haven't read the X-Men issue, so I'm lacking the context to give any sort of meaningful opinion on this.
But inherently I don't believe that her identifying herself as a mutant or citizen of Krokoa would necessarily mean she's not also african. Theoretically there's no reason she can't be both. I know plenty of people who identify themselves as American for example... but they also identify themselves with their own ethnic background. Being American doesn't automatically mean someone is no longer Chinesse or Russian or whatever. And I think being a mutant would largely work the same way. Theoretically at least.
Again, I didn't read the X-Men issue, so I'm lacking context. But the notion that she must be either/or rather than all of the above seems sort of puzzling to me. Maybe it wouldn't if I bothered reading the issue.