This happens at the flash tube. Different flashes of similar energy storage capacity will produce different amounts of light, based on the flash tube's ability to convert energy from electricity to light. This explains the frequently large disparity in the price of flash tubes. Energy that reaches the flash tube, but isn't converted into light, is converted into heat. The second often-overlooked contributing factor is the reflector.
Light leaves the flash tube in every direction.
The angle and finish of the reflector determine how the light is focused toward the subject. This also determines the final output of the flash system, since the narrower the angle and the more polished the reflector, the more light will be directed toward the subject. For these reasons, flash units of similar watt-second ratings produce different amounts of light. There is no standard for flash manufacturers to follow in terms of what the normal degree-angle reflector should be, or what finish the surface should be. This makes it difficult to compare flash units strictly by reviewing their literature.