Inanna (later Ishtar, Astarte, etc.), the Sumerian goddess of war and sexuality, was said to also appear in a male form, and to be able to transform males into females, and females into males.
There even was a sculpture found in an Ishtar temple at Mari of a very female looking musician with a male name who is assumed to have been a priest of her - that at least would imply that people of nondual gender had some way of being integrated into society at that time, but it of course is unproven. Normally, devotees chose a deity of the opposite sex as their main deity in Sumeria.
Then there are goddesses (and similar) who are "masculine" in that sense that they insist on having the active part in sexual intercourse, especially Lilith, and also Kali. I take it that you already know those two well enough.
And, not exactly a goddess, but I recall some Norse saga where a woman inherits the reign over their country from her father or husband and from then on gets referred to with male pronouns and acts as a male (but retains the female name). I don't remember the details.
Being genderqueer myself (born female), I think this topic might be of inspiration for me as well.