Hello onuralp,
Thank you for using our toolbox!
Indeed the DEVKIT uses the OpenSDA as debugger. But for this board it is also used as an USB2Serial.As far as I understand, you want to use the MCU without this OpenSDA on your custom board. You can use any USB2Serial for flashing the mcu by using the same UART pins. Also, you can use the JTAG& S32DS for Power Architecture to program the flash but for this you need to manually flash the .mot file after the Simulink built the generated code.
Please send me the EVB revision in order to tell which are the UART pins needed to be connected.
Hope this helps,
Marius