I agree that THEORETICALLY an Engine Dyno is the best way to measure power at the ENGINE. However, that's not to say that there are as many innaccurate engine dyno's as there are chassis dyno's. It is no different. I shall not be specific, but why do the results have to be gospel just because they were measured on an engine dyno? It may not have been properly calibrated to 10 years. Infact it is so much easier to 'fudge' the figures on an engine dyno, by altering any one of the many cell parameters that are controllable by the operator.
At least on a chassis dyno the car runs in its 'road trim', with all the ancillaries that it runs on the road. Not a dyno-specific exhaust, cooling system and so-on.
As said above, the 50psi thing is what DD have discovered to be the best pressure for consistency. Similarly, their system was designed to use 3rd gear, so we don't question it. Those who use 4th gear on a DD Dyno might aswell have not paid Dyno Dynamics prices and just gone for something cheaper as by altering the suggested methods, you are simply providing an inaccurate figure.
On the tests we have done, the car usually produces the expected figure in 3rd gear and, believe it or not, a lower figure in 4th!!