It might seem cockeyed, but I don't see why that's a problem. One could just as easily say that it seems cockeyed that a condition whose only symptoms are stress, social discomfort, and possibly suicide should be called a medical condition rather than a mental disorder. But who cares? Unless one stigmatizes one over the other, it shouldn't matter on either account.
Nature loves creating exceptions to our rules. In a world that has animals that photosynthesize and plants that don't, indeed a world that has humans with female brains that produce male gametes, why should we have any problem accepting the possibility of a mental disorder that is treated by conventional medicine?
"The world of our imagination is narrower and more special in its logical structure than the world of physical things." -- Max Born