Howdy Andrew,
Thanks for your question. Your assumption about the nature of the “master” branch for Applications is correct - it serves as a label over the default branches for the projects in that Application.
Unfortunately, you cannot change that branch name as you can with the other application branch you create on the Application Settings > Application Branches page.
However, we share your concern and have identified this as an issue for exactly the same reason you mentioned. You can track one of the related issues here:
https://jira.sonarsource.com/browse/SONAR-13623
I hope this helps, let me know if you have any other questions.
thanks,
Aaron