That's it! Its a whole lot easier to drop and retrieve your anchor (in deeper water) from the side of the kayak. However, that's usually not the ideal anchor point (think pivot point) on the kayak. In a river anchor situation, you'll be taking the full brunt force of the river to the side of the kayak. This could easily make your day very wet, or worse.
Ideally you want to have your anchor point at one end of the kayak or another. This makes the kayak much more hydrodynamic and allows you to use as little anchor weight and scope as you need/can get away with.
The Trolley System allows you to drop/retrieve from the side of the boat, while creating an anchorpoint at the bow/stern of the kayak.