app.config.js

const targets = {
  AppOne: {
    name: "App One",
  },
  AppTwo: {
    name: "App Two",
  },
};

export default ({ config }) => {
  return {
    ...config,
    ...targets[process.env.npm_config_target]
  };
};

npm run ios --target=AppTwo

{
...
"scripts": {
    "start": "react-native start",
    "android": "react-native run-android",
    "ios": "react-native run-ios",
    "web": "expo start --web"
  },
...
}