Fate does indeed genderbend lots of historical male figures into waifus. This is lampshaded several times in FGO's main story as you encounter them (historical records say X were a man), but as far as I'm aware, for in-universe purposes these characters will regardless always have been women in the series.

In the context of this post however it's worth mentioning that in FGO, Da Vinci specifically comes out with exposition that they made their servant self in the image of the Mona Lisa, ie. regardless of the "real" Da Vinci, their outer shell is now that of a woman. This is the basis of the 'terf bullshit' claim in the post, that these two exceptions of a definite male existence inside someone who is female on the outside aren't male, and it's transphobic to say they are, even when the story straight up tells you so.