The assumption that Scott's making is that "girls" and "boys" are semantically equivalent in this case. They're not. There's various ways in which the symmetry is broken, but the most basic one is that Mark's a straight man. When the overwhelming stereotype is that "we" as a community are heterosexual males, using "we" as a shorthand for "People who are straight men" is unfortunate because it supports that stereotype. Using "we" as a shorthand for "People who are attracted to men" doesn't. Unsurprisingly, this results in a fairly significant change in who's going to be offended.
Whatever his intentions (and I could easily believe that it was a slip of the tongue), Mark managed to imply that the Linux community is entirely made up of straight men. This is possible because straight men do make up the majority of the Linux community. In contrast, Scott's version doesn't succeed in implying that everyone in the Linux community is attracted to men because it's blatantly obviously not the case, so we know that Scott is using "we" in a different manner. Context is important, and unless you can invert everything else about the situation as well then simply replacing the word "girls" with "boys" doesn't give you any meaningful insight into whether or not people are justifiably offended.
In a more general sense, I'm saddened by this case because I think it's a clear case where the Ubuntu code of conduct could have been used to good effect. "Be excellent to each other" ought to include accepting that you've offended other people without meaning to and making appropriate restitution. If the offence was unintended, an apology should be cheap. Whatever the reality of the situation, failing to provide that apology gives people the impression that either the offence was intended or that Mark doesn't care about those who were offended. That's not a good way to build an inclusive community.
 Mako's original summary of the code of conduct