The two deities that probably come to mind the first might be Hapi or Neith. Hapi is almost always shown with large breasts, a sign of his fertility. And Neith is almost always portrayed like a male even though she is female. I also think Sekhmet was once portrayed as a male… Not sure if that counts as different in the gender area, but I do feel like it shows a sort of… blurring of gender boundaries.
Set would probably be a good choice, too. He’s all about breaking rules and boundaries - which I personally think gender roles and identities could be a part of that.
Atum has an epithet of the great he-she. Not sure if that would count, either? I always personally felt that that epithet showed ambiguity in the gender arena.
And for those interested in it, we’ve got Horus, Set and Thoth who are canonically bisexual (or possibly pansexual, depending on how we want to define things). And it’s my personal opinion that Osiris and Ra are as well.
I feel like most of the gods in our pantheon would be okay with their devotee being trans, though. It seems like they’re all very big on being true to yourself and I’ve not heard of anyone being pushed away from our gods for being MOGAI.
Not sure if anyone else has any other deities to add to the list?