Mouse and keyboard are shared devices in every OS, i.e. keyboard input is sent to the window having focus, and mouse messages are sent to the window under the mouse cursor. Special key combinations can be handled by the OS, like CTRL+ALT+DEL, or a program hooked into keyboard input, or they can be ignored (discarded) by the focused window.
That's why the device should be distinct from other devices, so that an application can connect to it exclusively. With the current serial driver every COM port has its unique number, so that each can be attached to a different application. As suggested by JMeller the input codes can be sent over the standard Serial USB connection, so that they are not misinterpreted and/or routed in the typical OS way.