How can you 'store' anything in something as ephemeral as environment variables? Where do these environment variables come from? When are they set?
You should of course store everything in version control; the point of this guideline is that the scope should not be the same as the app or an instance.
There is particular tension between this guideline and X. environments should be a similar as possible and I. there should be a single codebase for all deployments.