If you read into the SEC filing on how the deal is structured, it all but solidifies that Atlas/Southern will remain a contractor for many years to come. The deal is structured where GECAS owns the airplanes and leases them to Amazon. Amazon then leases them to Atlas/Southern where Amazon retains all the flexibility.
This deal really highlights the significant threat of massive layoffs for the pilots of Atlas/Southern down the road when/if Amazon decided to start up their own airline.