NTA

I might be wrong, and it might depend on how you said it, but it doesn't feel like you're trying to downsize her African heritage but just to explain that people won't see it on her and that's okay. It's part of her nonetheless.

Your wife is probably frustrated because you're right, it's not something people would expect and that's why she will be dubbed "white" for the rest of her life from outside perspective.

The important part is that the daughter herself will know that about herself and if she looks into it that the information will be available to her.

There's a lot of comments saying you're TA for downsizing this part of her culture but you're really not.. I myself look Russian but am completely mixed, like seriously, Hispanic and polish grandmothers and middle Eastern and Hungarian grandfathers.

You're being blunt and she will get it (or I hope so).