Good point, of course. And I think it all depends on the style. A legit soprano song can usually be easily sing by a legit tenor, or vice versa - but something with more of a pop/belt range wouldn't be as easily translated - you'd have to transpose it. Of course, not all auditioners realize that.
For me, though, it's more about what the auditioner's choice may mean. Is it just the case of wanting to sing a great song that happens to be written for a female character? Is it more about wanting to identify with the opposite gender (and what role does that choice play in a general audition call)? We are certainly seeing more productions that are experimenting with gender bending - but what if someone is auditioning for a "traditional" production that won't call for that?
Of course, if it's an older standard (those classics that routinely get sung by both genders with no real connection to show context) or a pop/rock song (which again, may often get "covered" by both genders), it's a different story. But if a guy comes in with "Shy" or "Everything I Know" or "Home" (The Wiz) etc - will the majority of directors be "gender blind" or will they spend more time wondering what the auditioner is wanting to say by making that kind of choice? I think it can be a tricky thing to pull off well without wanting to say "why did you pick that song?"