I think if you named your new skin ZZZZ it would override it, but this is not really a good idea, we need to resolve this the right way. By declaring the dependency it should work. Hopefully Tony or someone will chime in and explain this to us again.
To create your own custom skin: follow my tutorial here:
http://xcartguru.com/tutorials/x-cart-5-tutorials/building-a-custom-skin-in-x-cart-5/
Then you could just copy the skin files into the proper directories. But PHP class files that you have created in XLite/Module/XC/CustomSkin/ will need the namespace edited in order to work in the new module.
Creating a custom skin is my preference rather than using the default custom skin module. Allows you to develop multiple skins, switch between them, pack them up, and reuse them easily.