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The reason for the heater bypass is you never want the water in a running engine to stand still, that causes hot spots and localized boiling of the coolant which causes steam pockets to form. Thats the reason you hear some guys complain about never being able to bleed all the air out of their cooling system, its not that theyre not getting all the air out, its because of the steam is forming new air. I dont recall ever seeing a stock vehicle that didnt have some means of circulating water through the block while the thermostat is closed to prevent this. As long as you have some way for the coolant to keep flowing through the block you will never have this problem which is the reason guys with gutted thermostats or water restrictors dont have problems
