Code pulled from GitHub or NPM can be audited and it behaves consistently after it has been copied. If the code has a high reputation and gets incorporated into bundles, the code in the bundles doesn't change. If the project becomes malicious, only recently created bundles are affected. This code is pulled from polyfill.io every time somebody visits the page and recently polyfill.io has been hijacked to sometimes send malicious code instead. Websites that have been up for years can be affected by this.
Docker Swarm encryption doesn't work for your use case. The documentation says that the secret is stored encrypted but can be decrypted by the swarm manager nodes and nodes running services that use the service, which both apply to your single node. If you're not having to unlock Docker Compose on startup, that means that the encrypted value and the decryption key live next to each other on the same computer and anyone who has access to the encrypted secrets can also decrypt them.