a good question. FIrst you must understand diferences between shell, console and terminal. You are connected to Galileo or Edison remotely, this is why you need to use terminal (putty) to run commands on Galileo or Edison. Serial port with UART is standard technologies to use. This because of historical reasons and this communication is very simple to implement.
Why do we need special cable for this communication? Because motherboard manufacturers decided not to implement serial ports anymore and now we need to use cables that can be connected to USB ports. Most users do not use them, but we are not one of those. If you would have computer with serial port you would only need 3 wires between your computer and board to communicate (GND, RX and TX).
Regarding USB-client micro-B to USB-PC as you described it is used for Arduino environment. This way of communication is not something I have seen before for embedded platform. Intel probably implemented this interface for users who want to use Arduino environment.
Most embedded systems have an option for serial communication using terminal, while Arduino interface is not standard. Also the difference is that Arduino interface allows you to transfer files (sketch) to galileo, while serial interface only allows you to use bash commands.
I hope this helps.