To be clear, EnvKey is completely based around environment variables, so you won't need any EnvKey-specific code in your app apart from a line or two to install/import the package.
In code, config is accessed in the same way as local environment variables. For example, with python, it's just:
$ pip install envkey
# in main.py (the entrypoint of your app)
import envkey
# anywhere else in your code
stripe.api_key = os.environ["STRIPE_SECRET_KEY"]
If you decide to switch to some other approach based on environment variables, all you need to do is remove the envkey package. Does that help to address your concern at all?