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Driving a TCM2209 board with an Arduino?

The company I work for has a product that needs a test rig for some stepper motors that use a Trinamic controllers.  The TCM2209 board will successfully drive the steppers, however the boards lack an input (which I can see) to allow a stop switch input (from the motors assembly).  In hunting around the website I have found a method of using an Arduino Mega and a TCM5207 board.  This set up would be ideal, as it would allow the Trinamic driver to the Motors and the ease of input via the Arduino.  However I believe the board runs at 3V3 and the Arduino runs at 5V, can this be altered by moving the zero ohm link below the pair of jumpers like the TCM5207 and following the HOW TO DRIVE A STEPPER MOTOR VIA UART WITH YOUR ARDUINO MEGA USING A TMC5072-EVAL to give access to the motor?