Before this option we had to enter each channel on a system...up to 28 frequencies per system. With Control Channel Only we only enter the two or three control channels. 'Saves us some time, and saves memory in the scanner.
Early trunking scanners needed all the trunked frequencies for the radio to follow a conversation. Then control channel only came along, allowing you to program just the control channel frequency (and alternate frequencies that the controller would use) and track the voice frequencies as reported by the control channel data.