Protected Branches not working for blank projects in EE

In 10.2 When creating a blank project and either:

• Creating a file in the web UI
• Pushing a local repo to the remote repository

Results in the default branch (master) not being considered protected.

We can see that in later versions this is no longer the case by looking at https://gitlab.com/gitlab-org/gitlab-ee/issues/3968#note_51433729

As @DouweM suggested in https://gitlab.com/gitlab-org/gitlab-ee/issues/3968#note_51451210 this might be related to the EE specific feature that allows you to protect a branch and only make it available to certain groups or users.