To be fair to Johannes, I think he ultimately made the right decision. The main problem lie in communication, and timeliness.
Her comments cover everything from "trans women are mostly autistic boys who have been gaslit" to "there are only two sexes" to "trans people are unfit to play in their gender's sport." However, there are far worse comments floating around out there that talk about genital mutilation and all kinds of other heinous shit.
So...while biology does account for male and female reproductive systems across a variety of species, they have found that, as they continue to study many different forms of life, that they actually have to keep adjusting the model of what they once thought. Life is weirder, more complex, and accounts for a tremendous amount of variation in how this whole thing works.
I'm not a biologist, there are experts who can speak extremely well on this subject. Within the field of biology, the whole "two sexes" thing is kind of an oversimplification. Even if we just focus on humans and not, say, some form of algae with 500 different sexes, there are plenty of divergent forms of human beings that manifest as some form of intersex, with quite a few different variations.
Even if intersex people are a fraction of a fraction of the population, they are a compelling case study for why things don't definitively boil down across some kind of sexual binary across the board for absolutely everyone. Heck, even males and females in the traditional sense of sexual dimorphism tend to exhibit traits of the other sex in one way or another.
TL;DR - it's a huge complicated can of worms, and people who try to shutdown discussion of nonbinary or transgender identities with "there's only two sexes, it's just science!" tend to have a grade-school understanding of biology.