Must admit that puzzled me too, but I certainly use more than three litres when I change the oil so maybe the manual assumes you leave it on the centrestand and screw the drain plug back in as soon as the flow slows.
Like most people, I try to get as much of the old oil out as possible.
Either way, a 4 or 5 litre can of oil is usually a far more economical way of buying the stuff than individual one litre bottles. Beyond that, it doesn't really matter... just fill it until it is at the top of the sight glass, run the engine for a bit to fill the filter, wait a bit and check/top-up the level again.