UART is used for sending the debug information to the host through a USB 2.0 cable. This is done by making use of a USB-Serial Converter chip as shown in page 8 of the SuperSpeed Explorer Kit Schematic.
IO(53:56) refers to GPIO 53:56 of the FX3 chip. Please find the pin description for FX3 chip at page 15 of the FX3 Datasheet. The link to the same is given below:
From this, you can understand that when the GPIF bus width is configured to be 32 bits (as done by this example project), GPIO 53:56 can be used as COM port. If the GPIF data bus width is configured to be 16 bits, then depending on the io_cfg.lppMode, GPIO 53:56 can be used as UART/SPI.