It's not just in the "today's" Training Command that "upside-down" selections happen. In early 1971 there was a huge pool of folks awaiting F-4 training at Miramar and Oceana after winging. Only a very few guys got RIO slots out of VT-10, and (due to some factors I never understood) usually it was the bottom guys of the class got those slots. All of a sudden, there was a huge vacuum in the pipeline, plus the higher-ups in the fighter community wanted some of the top studs to go RIO. Result... almost half of my VT-10 class went to Glynco to be RIOs, as well as the class just after mine. Folks who were in the top 10% of the class got their 4th choice... and folks in the bottom 10% got their first choice... also the first choice of the top 10-percenters.
Needs of the Navy always prevails.