Sequencing modes for FCC "Intentional Radiator" test
Is it permissible to use software to sweep each of the data rates (say
  at one rate per second) and check for out of band exceedances during
  that time period?


I doubt there is a rule that you have to walk to the device and reconfigure it and then run another test. However, the product needs to be tested in multiple configurations (like powered or battery mode) and a debug cable is probably not going to be an option because it changes the products configuration. So if you can switch the modes wirelessly (without using another software mode) then this would be probably be acceptable. 

But if you already have a quote for time and they don't charge addtional hours, why would it matter? If they charge for extra time, then its in your best interest to make sure the testing goes as fast as possible.