It may seem obvious but it is still incorrect. In a sense you have touched on the answer in relation to the flue.
Short cycling directly increases the boiler temperature (in that the heat is not been dispersed from the boiler quick enough), thus increasing the flame chamber temperature thus increasing the flue temperature. Flue temperature is directly proportional to efficiency, which is turn is directly proportional to fuel consumption. The higher the flue temperature the lower the efficiency of a boiler and thus more fuel will be wasted to the atmosphere and not into your home where it should be going. For example a standard efficiency boiler will have on average 200C flue temperatures. A high efficiency condensing boiler will have a flue temperature of approx 50C. The extra heat is being transferred into the heating system and thus being more efficient.
To check this have the boiler running with all radiators open and check the flue gas temperature with a FGA and then close down most of the radiators. An distinct increase in FG temperature will occur.
As I previously stated, another directly proportional side effect of consistent high boiler temperature is component failure. Metal expands as we know when heated. It generally reverts back to it designed state when cooled. Heat excessively and it does not, leading to undesired performances and eventual failure. This brings unnecessary cost to the homeowner.