Isn't what you described here just a variation of chromosomes? We know there are more than two combinations, but Sex is still determined binary via the existence or absence of the Y chromosome, no?
Most people typically look at genitals to determine sex. However, as beeforpork pointed out, there are individuals with XY chromosomes who have a vulva, a vagina, and internal testicles. Based on physical appearance alone, which is often the basis for sex determination at birth or during annual physicals, they would be classified as female. Yet, their chromosomes tell a different story. This complexity suggests that it may be inappropriate to strictly categorize them as either male or female. This is what it means to be non-binary. Beeforpork did a good job of detailing other instances where biological markers of sex don't align with the so-called sex chromosomes.