Does dotenv contradict the Twelve-Factor App?

I have read about the Twelve Factor App's Config - Section III and searched for a way to do it in NodeJS. It seems that most people recommend dotenv to store configs in environment variables.

However, it seems that dotenv contradicts the Twelve-Factor App, as states:

Another approach to config is the use of config files which are not checked into revision control, such as config/database.yml in Rails. This is a huge improvement over using constants which are checked into the code repo, but still has weaknesses: it’s easy to mistakenly check in a config file to the repo; there is a tendency for config files to be scattered about in different places and different formats, making it hard to see and manage all the config in one place. Further, these formats tend to be language- or framework-specific.

The twelve-factor app stores config in environment variables (often shortened to env vars or env). Env vars are easy to change between deploys without changing any code; unlike config files, there is little chance of them being checked into the code repo accidentally; and unlike custom config files, or other config mechanisms such as Java System Properties, they are a language- and OS-agnostic standard.

Making sense of this statement, it seems that using dotenv, you will create a config file .env which will then export them as environment variables.

Wouldn't this violate the Twelve-Factor App, since the .env file can get accidentally checked into the code repo?

via StevenDaGee