Regarding USB C you are right that there are four differential pairs on the connector. However, for communication only two pairs are used because the USB 3.1 protocol only uses two. On the device that has a USB C connector you need a dedicated controller that manages the orientation of the plug. Then the two data lines are connected to the right pins on the connector through a multiplexer. The other two pairs on the connector are for no use in USB mode but if you want to use USB C in alternate mode (e.g. DisplayPort), signals can be rerouted.

You can find all the information on usb.org (zip archive with full specification).

This basically means that the EOMA68 standard has two differential pairs that are not used for USB but if your intention was to make it available for USB C, an internal multiplexer would be needed.