This whole thing was created because it's annoying for devs to set up Vault, but Vault is an Ops process, not a Dev process. Just use environment variables and let Ops take care of exporting them via a credential management system. Coding a specific credential management system into your app is a bad idea.
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?