Your statement is fictitious. There is no instance of intersexuality in the real world. But labeling genital-birth -defect afflicted as non-binary is instead very offensive for non-binaries and for them, since you're just assuming they have gender dysphoria over it and implying that non-binary identifiers MUST have genital defects. A child has no concept of sex. They can't identify as gay and therefore anything since they are realistically not ready for sex unless you're a pedo.
If the creator of this game really intended for the character to be non-binary, they should have made them with characteristics of both genders.