Did you become a safer pilot as a consequence of conversion of your licence to Part 61 licence, Sunfish? What is the safety benefit of Part 61?
Nobody's advocating that CASA shouldn't have procedures to confirm, and record confirmation of, satisfaction of the requirements for the issue of a permission (provided there's some safety justification for the permission, which is a related but separate question). But those procedures should include recording, on the file, all relevant correspondence, including notes of all telephone calls, from the applicant.
This isn't the product of reasonable and competently-applied bureacratic procedures:
Frustrating thing was each time I called them to confirm receipt of the application, first two they said 'it is received, allow two weeks for processing'. Both times I left it for 3 weeks and then called to be told 'no record of that in the system.'