The software would not be preventing non-approved transmitter behavior if the software supported the loading of custom firmware that can implement non-approved transmitter behavior. Here is the full paragraph from which you quoted:

  Manufacturers must implement security features in any digitally
  modulated devices capable of operating in any of the U-NII bands, so
  that third parties are not able to reprogram the device to operate
  outside the parameters for which the device was certified. The
  software must prevent the user from operating the transmitter with
  operating frequencies, output power, modulation types or other radio
  frequency parameters outside those that were approved for the device.
  Manufacturers may use means including, but not limited to the use of
  a private network that allows only authenticated users to download
  software, electronic signatures in software or coding in hardware
  that is decoded by software to verify that new software can be legally
  loaded into a device to meet these requirements and must describe the
  methods in their application for equipment authorization.