Look at it this way. If CASA (or anyone) believed the BMI was an infallible and absolute measure they would bin your medical based on that alone. They know its only an indication of a possible issue, so they arrange a real world test, the results of which supersede the BMI.
With regards to the lousy service, I would suspect staffing levels. When I had an issue with my medical a while back there appeared to be only two people processing medicals for the whole country. Any issue with a medical seems to involve a lot of frustrating waiting and stress, just what you need.