Using the Teensy Ports is best for Teensy as it uses PJRC optimized code to talk to Teensy units more effectively at higher output rates, especially the T_4.0 that runs maybe 20 times faster?
That interface is also more effective at reconnecting the Teensy and computer from 'offline' after uploads or disconnects.
Indeed either can work - but if you run into trouble in the Teensy Ports - it is code Paul can directly edit and correct.