Since gender identity and genetics don't always match, whether a person's gender is determined by their genetics, their dominate sex organs, the doctor that witnessed the birth or through a person's own self-identification of their true gender, WikiTree should, at the very least, support the genetic identity as much or more so than a person's assigned gender.
Having a gender identity for genealogical purposes (male/female) follows the traditional genealogical structure, but it would be apropos for WikiTree to provide a field on the DNA testing page that identifies a person's genetic identity. If the ability to enter Y DNA tests has to be gated (why? to prevent a bad upload of data? this seems unnecessary as nothing prevents a bad auDNA/mtDNA upload in this way), then the gate should be on genetics not gender identity.
A new field on the DNA testing page that is a drop-down that is auto-populated from the gender field on the profile (male=XY, female=XX), but allows someone with more genetic information to select more specific genetic identification such as XXY would be beneficial and set WikiTree apart. The genetic testing upload availability could then be based on this field rather than the gender field (if that is truly necessary).
Of course, the easiest solution would be to remove the gate that prevents a female from upload Y DNA. :)