Override variables set by custom config file

[ddukic]

Is this intended to be like this or it is a bug? I followed Switch-between-multiple-configuration-files guide to setup my config files for different environments.

If I run npx cypress run --env fileConfig=qa while having set variable something=bar in the OS level it will not override the value from custom config file which looks like this.
{ "baseUrl": "https://qa.acme.com", "env": { "something": "qa" } }
If I remove the key-value pair something from the config it will use the OS variable and if I set the something in cypress.json it will work, but it doesn't override the value from the custom config file. Is this a bug or intended to work like this?