your engine does not have a drain on the block meaning that about a litre of water/coolant is always stuck in the block, the only way to rid of it is to flush with clean water and add concentrated coolant first to the engine and top off with water.
e.g. if you definitely know that your engine takes 4 litres of coolant/water mix and you have drained from the radiator and flushed with removed thermostat then you should add 2 litres of coolant conc (if you want 50%) and top off with distilled water, that way when you start the engine the water in the block will mix with the coolant and you would have proper concentration.
anyway - if you had rust then an acid flush (citric) is required to remove the scale and buildup in the system, then add your fresh coolant mix. If rust is present then cooling capability would be severely hampered. Also check the metal coolant intake pipe at the back of the engine with a mirror and light, if you see it has flakes of rust hanging from it, renew it immediately. It would be stopping cold coolant flow and also will leak anytime soon.