Control Cabinet Drawing

I've attached an initial revision of my control cabinet and how I'm going to put mine together. Since I'm using the Teensy4.1 and the latest AR4-MK4 software I will likely also wire in the support for MODBUS. Especially since I have the software tools from https://www.modbustools.com/ for both master and slave. But I also want to add CAN bus support so the drawing shows how I'd use pins 30,31 (CRX3, CTX3) and switch the J5,J6 limits to 32,33.
The problem is that I see in the newest Teensy4.1 code that these pins are assigned to J8 step/dir. If I switch the declarations in the Teensy4.1 sketch and remove references to J8 will that confused the HMI software running on the PC?