Best way to build a seperate Cordova app?

Hey guys,
I have a little question about the Cordova implementation. Is it possible to build a seperate Cordova app which is still linked to the current deployed version on the server? In my case I need to build a “special release” for an alternative app store. I need to hide some menu points if the user uses this version of the app. So it would be great If I could set a variable within mobile-config.js which gets injected into the Cordova build. Within my app I want to check if the variable is set, f.e. window.cordova.IS_ALTERNATIVE_STORE === true.

Any idea how I could solve this? My first thought is to add an own Cordova plugin when building the alternative version and removing it when I build the “standard” version of the app.

Here is what we did: use env variables to customize the mobile-config js script / build scripts.