Not exactly sure to get all the complexity without seeing code but, if you need a JSON for your configuration, it is possible. I had the need to obfuscate some value from my repository, therefore I created a JSON which is then injected into the configuration. You can maybe follow the same logic to inject different values for the environment?

I documented this in another blog post: https://medium.com/stencil-tricks/hide-environment-variables-in-your-stenciljs-project-b327cda6ad3e

Not sure it exactly answers your question but hope it helps.