Charging for a “flush” is a way of padding the labor bill, the tech receives one hour of labor for this.
My co-workers often charge for a cooling system flush during a cooling system repair however these vehicles are drain and fill, I have not seen anyone touch the cooling system flush machine in the last 10 years.
Using the flush machine is a less effective method of replacing the coolant, the water pump mixes the old coolant with new during the flush process.
BTW you won’t find rust in an aluminum engine.