I know who to believe: the car that was dynoed 4 times. Each time at two different dynos the belly pan was never removed. For a straight dyno pull there is no need to remove the belly pan.
Whipple should be able to strap the car down without removing the belly pan. Also removing the belly pan, as in an oil change does not take any where the time they quoted. Actually the rear two belly pans are removed for an oil change and still takes less time than quoted. An oil change takes 2- 2 1/2 hours including changing filter, draining, refilling, lifting twice, removing pans, etc.
The other reason not to remove a belly pan unless necessary is the potential of stripping the screws which is easy to do.
If Whipple has a problem have them call Bob Ida @ Ida Automotive in Morganville, NJ and learn how it can be done without risking the car. The probbaly know Bob from SEMA shows and elsewhere.