Please refer to page 16 of FX3 datasheet to understand how the different pins are multiplexed. Link to the same is given below:
In your configuration, the isDQ32 field is set to false which indicates that the data bus for GPIF II block is not 32 bits. Also, the lppMode is set to CY_U3P_IO_MATRIX_LPP_DEFAULT which indicates the default LPP mode where all the peripherals are enabled. The corresponding pins can be identified by checking the column 16-bit data bus + UART + SPI + I2S from the table provided in page 16 of FX3 datasheet.
According to this, the UART block for your configuration will be available at GPIO[46:49]. If you are using CYUSB3KIT-003, then the UART block is to be made available at GPIO[53;56] to have a Virtual COM port connection established. This is because the hardware of the Explorer kit is made in such a way that the GPIO[53:56] is connected to a USB-Serial chip.