Coolant bypass

Can anyone explain to me why we have the coolant bypass tube which runs underneath the intake manifold? If coolant is cycling as it should then wouldn't it warm up faster without the bypass. Real curious since I'm putting plans together to fabricate a custom intake setup and needing to understand what, how, and if/why it will be necessary to retain the bypass.

Until the thermostat opens, there isn't any flow of coolant within the engine. The "coolant bypass tube" isn't so much a coolant bypass, but a thermostat bypass, which allows hot water to hit the back of the thermostat and cause it to open sooner as a result.

Actually, the coolant is circulated throughout the engine whenever the water pump turns. The thermostat only lets it out to cool off in the radiator. If you have an oil cooler, then the bypass hose is needed to provide flow to it. There is a second port on the intake that supplies hot coolant to the heater. If you're not running an oil cooler, or a heater, then you can build an intake manifold that goes without these provisions... otherwise, I'd keep the design similar to the stock cooling scheme.
http://www.mazdatrucking.com/B2200/B22CoolantFlow.html

Actually, the coolant is stuck wherever it is in the engine until the thermostat opens. The water pump cavitates but can not circulate the coolant fully until the thermostat opens. The bypass is there to allow minimal coolant flow until the thermostat opens, giving the coolant a place to flow. That is why you don't get heat to the heater core until the thermostat opens. The water pump sucks up water from the lower radiator hose, and can't do that until the thermostat allows it.

Well, I won't argue with you... you can believe what you want.

I thought that the water circulated between the block/cylinder area, head(s), and the intake even with the thermostat closed. Which is why I was thinking the engine would warm up faster without the bypass. I don't have an oil cooler but I do want to keep the heater. My thoughts were to delete that section in the fabrication of a new intake. Besides I always thought Mazda could have done a better job than running that little U bend hose at the front of the engine.

You are correct, but the coolant's job is to cool the engine, and lower the freezing point to keep from destroying it in severe cold temps. The engine will warm up just fine without any changes. If you want good results from your heater, a thorough system flush may be in order.