Thanks for the feedback!
There are two possible issues you maybe hitting:
1. QR reader may not be able to run the link in a proper way - we figured out, the hard way, that some QR readers are not opening the nativescript:// protocol, but instead are starting a search in google or bing. To fix this we will add a QR code reader directly into the companion app at a later stage. For the moment the QR code reader that we know that it works for iOS and Android is called Red Laser (https://itunes.apple.com/en/app/redlaser-barcode-scanner-shopping/id474902001?mt=8
2. The second issue you maybe hitting is a bug in the iOS companion app that do not allow deployment of more than one app twice. In this case you should uninstall the companion app and install it again every time you want to deploy on the device :(. It is very inconvenient - we are working on fixing this ASAP, so expect and update very soon.
Other than that your expectations are correct. Once you have installed the companion app it should understand the "nativescript://" protocol and should open when QR reader scans the url.
Please let me know how it goes and if these recommendations are fixing the problem for you.