That's not what that line means at all. That line means that an argument like `let's stop using gender-neutral language in our documentation, it's easier to just say "he" instead of "the user"` won't fly: this type of argument prioritizes the comfort of a privileged group (males) over the safety/well-being of a marginalized group (women and non-binary people).

I'm all for being gender-neutral for the sake of neutrality, but the idea that the use of "he" somehow hurts people's safety or well-being sounds a bit absurd to me.

You are going to have to explain how using 'he' can harm the safety and well being of somebody else.

That is a complete misreading of the clear statement that text is making!