The only advantage of running it on in a garbage can under water, is it also tests the unit for leaking exhaust fumes backing up into the motors inside cowling. While if on muffs, there is no back up pressure for the exhaust hence unable to tell if you have exhaust leaking into the cowling. And of course, less water usage on muffs depending how long you ran the motor.
You might want to do some measuring before slapping the LU back on. If the water tube is short and unable to mate with the water pump housing, you will not have cooling water to the engine block and can result in some serious damage to the powerhead.