operating Arduino mini pro based custom module from GPIO

Hi All This is my first time posting on this forum so please forgive me for potentially mis-posting under the wrong topic. I am currently in the middle of a project that involves raspberry and a ATMega328P based Arduino board that act as a slave. The board is called pneuduino and further description is linked here My question is : can I control a arduino board through FTDI - GPIO pins communication or it has to be a serial port connection? Thank you in advance for your time and attention. |500x400

The "FTDI" header is connected to the serial pins!

Is there a reason you can't control it via serial using that? I think that's the intent of that board.

Thank you for the reply. The reason that i prefer GPIO control is that i want to integrate this set up into my existing IOT system that is programmed for GPIO control. Because i dont see how to integrate MQTT capability into this pneuduino board so I think i will have to control it using raspberry instead of having it run independently.