Try by making the io_cfg.gpioSimpleEn = 0;
You can overwrite them in your application using the API CyU3PDeviceGpioOverride
Also, CY_U3P_IO_MATRIX_LPP_DEFAULT enable all the LPP blocks. I see you are using only UART, then please change it to UART only. Else the GPIOs will not be available.
Please check. You can check the status of CyU3PDeviceConfigureIOMatrix API. If this is passing, you should not see any problem with the pin assignment