I wouldn't say the current solution is hard, or even especially work-intensive. All you need to do is to define alienDeployments for variants you want to add, then add an appropriate flag under the ufos section - voila, now your Battleship has a different set on weapons on board when crewed by Mutons. You can even modify the UFO's parameters, such as accuracy, when crewed by Mutons.
(Works in OXCE only.)