When I had my '12's MT rebuilt by Ford last year, one of the gear clusters was well, clustered, and it was replaced with the phosphate-coated 13+ set for that gear.
Phosphate coating isn't new to Ford. They did this for the 93 GT and Cobra T5s as well, similar concerns. It's a band-aid addressing an unlikely cause (gear facing wear) and it won't get at the root of the problems with some of these cars.
My opinion, borne out only by what lit up on my car, is that the bearings used in the trans
were of suspect quality or had poor quality control. I told Ford dealer that I suspected an input shaft bearing was hurting and that was causing the whines. They confirmed my diagnosis on disassembly.