I agree with most of what you're saying Slayage and this may sound like splitting hairs, but just to clarify, Allure is actually a women's magazine. The fact that Billy happens to be the first man (to my knowledge) to ever cover the magazine in its 29-year history should clear up any doubts.
Of course anyone can read or buy it, but Allure is a service magazine aimed exclusively at female skin. It is not a visual-driven magazine like VI. So unless they change course and start showing product/content tailored to male skin, meaning products that are actually formulated specifically to deal with the testosterone, thicker skin, higher collagen content, hair follicles etc of men, the magazine will remain binary.
I've not seen this issue yet, but it seems to me as though it's just another case where the magazine pays tribute to whatever beauty ideals Billy represents while highlighting what their (mostly) female audience can take from that. Just like GQ does with their Woman of the Year which may showcase women, but the target demographic is still men. Have no problem whatsoever with him getting the cover because as many pointed out it happens fairly often elsewhere.