Sounds correct.
The application (tinyG2) has no idea what is actually connected to the pins.
Since you only have 3 drivers, using the Gshield pinout will allow you to bypass for now recompiling with a different pinout model.
Keep in mind that DUE has no onboard port conditioning (pull ups, caps, etc) to when you move on to limit switches and other I/O, you have to take care of that.
And, as always – DUE is 3.3V logic. You may need to buffer or logic level translate
Also – you will have to set microsteps manually on the external drivers as well as power level.