Essentially the porting changes the port timing to match the longer stroke as well as enhancing flow. Along with that is a cylinder head mod that enlarges the combustion chamber to accomodate the longer stroke, preventing piston to head contact and optimizing shape and volume. This way you don't need the spacer plate.
But like the other guys said, with the Vito's kit, you can just slap it in and run it. Engine work like above is just a better way to go if you can afford it.