"We do state that we think “Aunt Tilly” shouldn’t be root on their own computer; they should instead pay a student to administer it and support them, and be mere users."
This is a perfect example of what I was talking about. In an environment where women are stereotyped as having little technical knowledge or ability, having the prototypical clueless user be a woman is a problem. It's not a huge thing. It's unlikely to leave anyone hugely offended or upset. It is, however, something that helps perpetuate that stereotype. Using it doesn't mean that you hate women or think that they're unlikely to be technically competent, but it helps create an atmosphere where people who actually are overtly sexist feel supported in their sexism and it contributes to women feeling that they're going to have to work harder to gain the same level of recognition.
Communities that feel comfortable behaving like this are creating problems. If they're unable to see them, it's because they haven't learned to look properly.