In case other people run into similar issues, I'll lay out what I've found today.

-The inconsistent output was due to the fact that when you open a serial connection with python, it resets the Arduino and so python can send signals without the arduino having finished its setup() function. If I put in a 1 second delay on the python side, inconsistency stops and I no longer run into byte errors at all. I'm looking into alternative means of preventing this reset since the time delay is a deal-breaker for me.

-The decode() function has a keyword argument called errors, which can be set to "ignore" if you want the code to just ignore things that can't be interpreted in your desired format. With just this keyword setup, I never got errors but output was inconsistent due to reset.

In case other people run into similar issues, I'll lay out what I've found today.

-The inconsistent output was due to the fact that when you open a serial connection with python, it resets the Arduino and so python can send signals without the arduino having finished its setup() function. If I put in a 1 second delay on the python side, inconsistency stops and I no longer run into byte errors at all. I'm looking into alternative means of preventing this reset since the time delay is a deal-breaker for me.

UPDATE: Replacing

arduinoSerialData("COM5",9600,timeout=1)

with

arduinoSerialData = serial.Serial()
arduinoSerialData.port = "COM5"
arduinoSerialData.baudrate = 9600
arduinoSerialData.timeout = 1
arduinoSerialData.setDTR(False)
#arduinoSerialData.setRTS(False)
arduinoSerialData.open()

seems to bypass the reset. I included both the setDTR and SetRTS functions here because although setDTR works for DUE, it seems some other Arduino boards need setRTS instead.

-The decode() function has a keyword argument called errors, which can be set to "ignore" if you want the code to just ignore things that can't be interpreted in your desired format. With just this keyword setup, I never got errors but output was inconsistent due to reset.