Initially it is mapped to have the SPI off. So the debug pins go to the UART debug chip. If you want to use the SPI you will need to configure the main settings as follows
io_cfg.useUart = CyTrue; io_cfg.useI2C = CyFalse; io_cfg.useI2S = CyFalse; io_cfg.useSpi = CyTrue; io_cfg.isDQ32Bit = CyFalse; io_cfg.lppMode = CY_U3P_IO_MATRIX_LPP_DEFAULT;
That will move your UART down to pins GPIO - GPIO and enable SPI on the old UART pins of GPIO -GPIO. This means that the SPI connection will be wired to the UART debug chip, and the new UART Debug output will be wired to nothing. So you wont get anything unless you connect another USB to UART chip like an FTDI Friend to the new UART output.
This will allow you to use the SPI though.
Yes, you are right. I saw the comments in the code.