JTAG interface was designed for on chip debug. That means, it can debug chips that has no bootloader at all. The board provided by JobyRobotics is based on FTDI chip that allows two simultaneous USB connections. For us it means that FLOSS JTAG allows JTAG and UART/COM connections.
Let's take a look at upper side of the board. It contains JTAG connector (which is connected on photo) and two sets of RX/TX LEDs for JTAG and UART/COM interface separately.
On the other side of the board there is 4 pin UART/COM connector, which contains: Ground (black), TX (yellow), RX (orange) and +5V (red)
Usage of board is pretty simple: JTAG can be used to upload firmware into the board and/or repair board with broken bootloader, and UART/COM interfaced can be used to make "COM port style" connection to the board. COM connection can be used for example for telemetry debug.