Being the female clone of a man doesn't make you transgender. You could clone a man and simply remove the Y chromosome to create a female clone. Said clone would have Turner Syndrome, but it would be female.

You could also go a step further and duplicate the X chromosome. I don't know what the consequences of having two identical X chromosomes would be, but theoretically she would either be totally normal or still have Turner Syndrome. We don't really know why Turner Syndrome happens, so the importance of non-identical genetic code in the Barr bodies is unclear.

It's actually a pretty interesting concept from a genetic point of view and works perfectly in a sci fi setting. What would be even more interesting would be a male clone of a female. Subtracting a Y chromosome arguably doesn't remove the "clone" status because there's no foreign genetic code, but does the addition of a Y chromosome mean he's not a true clone? What if they simply edited the SRY gene into one of the X chromosomes?

Fascinating stuff. I'm sure the game doesn't delve into it even a little and just uses "WOW TRANS CLONE" for shock value, but still.