Hi @yonas,
You can now use the output alias feature to not to overwrite (to alias/copy) output env vars, without any scripting! Related announcement: Monthly release of Bitrise CLI tools and summary of updates (May, 2017) - CLI v1.6.1
We’re also working on First class mono repo support , which can help if you indeed want to register separate apps instead on bitrise.io for the same repo. If you’d prefer that, please vote & comment there so that you’ll be notified once the feature is released! 
Of course if you have any questions in the meantime just let us know! 