It's currently only possible to use the username and app password as the credentials for authentication for the Repository Permission Update endpoints. 

This feature request is to implement the ability to use Workspace Access Tokens (WAT) for authentication in the following endpoints : 

• Update an explicit group permission for a repository
• Update explicit user permission for a repository
• Delete an explicit group permission for a repository
• Delete an explicit user permission for a repository

The same applies to project-level permissions.