How would you go about making a repeatable, automated deployment if you don't store configuration information in source control to load into the environment variables?
Doesn't this just push the problem up (down?) a level in the hierarchy? I mean, you still need to deploy these and configure them with the information the rest of your deployment requires right?
That link is talking about a problem with e.g. .htaccess and basic directory permissions, not a problem using git per se. But yeah, put that stuff in envars.
If there's any question, I think the rule has to be the former. There are standard, auditable ways to keep sensitive data out of git: .gitignore, environmental vars, etc. Once it's in git, any attempts to keep it out of a public repo will probably be manual and ad hoc.
If the organization is "closed" by default, i.e. it only rarely releases code to the public, this may not matter as much.