BitsAndDroids is working on a version of the program that can send and transmit without having to run two programs. He is also trying to get TX and RX running over one port, but from what I have heard it’s not trivial. Currently, you need two ports and he always uses one for sending and one for transmitting. So, it’s either the DUE or two Arduinos.
Mobiflight works with its own firmware, so I guess they solved it differently. It’s hard to say. But Mobiflight does not allow you to add your own code like BitsAndDroids does. That’s why I choose it, alltough the Mobiflight is much more user friendly.
If I understand you correctly you want to connect two Arduinos. But I am not sure I understand why. You want to send signals to another Arduino when you flip a switch, correct? But it should only send back to MSFS. And the receiving part should receive values from MSFS only. Otherwise you might run into snychronization issues. Or is this only to have more GPIO pins?
Yes, I am using both ports on the DUE. One for sending, one for receiving. I have one connector open for each port. And one program running for each port. This way sending and receiving is completely separate and the never interfere while running the program. That way everything stays in synch even if i flip switches in the sim or MSFS or the Arduino “looses” information.
No, I am not using a steering wheel to fly my plane. But my cockpit is multipurpose. 
