aoe3rules, the feminine used to describe countries and naval ships and whatnot is a holdover from when English was but cobbled Frenchish and Germanic languages and most nouns had an associated gender.
I'd support a change to "their", but I must say that feminism has far more important fronts than the Gamemaster message on a Diplomacy site. While "their" is strictly grammatically incorrect because it implies a plural, in many languages, including French, from which English shares a common ancestor, the plural is often used to imply a formal singular, such as with vous vs. tu. I'm not sure, but could the Queen's usage of "we" be a carry-over of this?
The masculine is historically gender neutral, but for patriarchal reasons. Honestly, I think I'm as annoyed as any of you with rigorous demands for PC, but it's only annoying because we've been raised with the non-PC terms. It still represents very little effort on our part, and it certainly could help combat unconscious denigration of women. I still think that more concrete movements are far more efficacious. I suppose it depends on how much you think language affects us.