Looking at the Magento 2 docs, you can override a base/core layout.xml file - http://devdocs.magento.com/guides/v2.0/frontend-dev-guide/layouts/layout-override.html
Is it possible to do so within a module rather than theme?
Alternatively, is it possible to bundle a theme within a module and extend that (and multiple other themes from multiple other modules) from the main website theme?