Is there a low profile water pump for a 360?

Yeah the cars had a 340 or 318 and the motor was farther back.
It has to do with what year it was built, not the displacement. Specifically, engines up through model year '69 cars had the shorter cast iron water pump. They also had a fan with the blades notched to better clear the 'bubble top' radiators.

With a fixed blade fan (or flex fan) there are a variety of spacers to position the fan distance from the radiator.
For a clutch fan, the options have been laid out above.
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Some dimensions here Fan clutch bushing question

Square top radiator made to work in a '67 along with a '68 radiator with a '70 bottom tank which replaced that setup.
340 radiator