The UART pins in FX3 can be configured as per your requirements. If you refer to table 7 in the FX3 datasheet, if you configure for a 32 bit data bus OR if you wish to use 16 bit DATA bus + UART only , then the UART pins are from GPIO[53:56]. To configure a 32 bit data bus, you need to set io_cfg.isDQ32Bit as TRUE and to use only UART, you need to set io_cfg.lppMode = CY_U3P_IO_MATRIX_LPP_UART_ONLY. In these cases, the UART lines will be on GPIO [53:56]. In this configuration, you cannot use SPI
If you wish to use SPI then you would need to change the UART lines to GPIO[46:49]. For this you would need to set io_cfg.lppMode = CY_U3P_IO_MATRIX_LPP_DEFAULT and io_cfg.isDQ32Bit as FALSE. This way you can use both the SPI and the UART.
Thanks so much for your detailed information!