I have come across an issue reported by a customer as follows

You don’t have permission to register applications in the Default Directory directory

Note that, Owner role is an Azure RBAC role and is not the one required in this case. For registering an application, your user should have an Azure AD directory role, which need to be assigned separately from the settings. Here is how you can assign the permissions for the users. Open the blade Azure AD– Users — Users Settings and enable the necessary settings as shown below:

With the above settings enabled, the users will have the permission to register the application in the Default directory