In cases where there exists a clear delineation between the engine being used to tell the story and the assets being used to tell the story - e.g. your average open source video game - it seems like a reasonable approach would be to use a separate content license for the assets in question.
However, it's possible to imagine a situation in which this distinction does not really exist. Imagine a story hosted on GitHub, for instance, about a rookie programmer learning how to develop in a new language told by means of the commentary present in the code, the commit history of the code, and symbolic usage of certain functions representing their development throughout. If you wanted to allow derivative works of this story, would you use a creative commons license; would one of the open source licenses be more appropriate; or would you need to use a combination of licenses to distinguish between the work of fiction and the produced code?