Everyone at the Unseen University knows that. They're all men, naturally, so they can't imagine any other way for it to be.
Just don't say it out loud around Granny Weatherwax, since she's prob'ly the midwife who delivered that man when he was very young, and the mother wasn't male either. We all get along just fine as long as the women have things their way, and the men have things their way too - the women's way, that is.
No one has the bad taste to comment on this arrangement until Eskarina is born, and a wizard makes a silly mistake. Could happen to anyone really - his dying moments unwittingly infuse the baby girl with wizardly, male magic.
In time, this brings the wrath Mistress Esmeralda Weatherwax down on the fortress of male magic, which is invaded and defeated never even knowing it was engaged. Saves a lot of work and running aroung that way, y'know. But Esme's real problem is that little girl, and her real problem is a little boy, and his real problem is -- unreal.
Neither the womanly witches nor the male mages are quite ready for this little girl with tomboy magic. Nor is she quite ready for herself.
As in Pratchett's other tales, the fun is in the telling. This battle of the sexes, like so many others, is fought to a draw - there will be cultural exchanges, visiting rights and such, and jittery kind of peace. All end up happy enough, but it's still one world with two peoples in it, male and female.
Except maybe for that girl and that boy. Male and female yes, in a child's way, but they have much too much in common.