The file system location of the default master template is set within a subsite's properties. To chage the look of the Main Subsite you should create a new master template and update the properties. To change the default look of all subsites you should edit the default master template.
If packages were to create their own master templates, even if they were just do-nothing stubs which passed properties on to the default master, then the look of individual package instances could be changed by placing an overiding package master template under the page root.
