I believe (just a guess) that the reason for the gains when removing the DPF is from removing the restriction in the exhaust. If you do this on a stock car, obviously the car has been programmed with the knowledge that there would be a DPF restricting flow. If you add a tune that has been programmed for not having the DPF, they can make the engine flow more air, have more boost, rev higher ETC without causing damage to the DPF or the engine.
Just like with the gas cars, if you put on aftermarket downpipes, not much really happens until you tell the computer that it CAN flow more air now. This is the reason that you can put some bolt ons to the N54s and gain 100 HP or more. The factory has to limit air flow with the factory IC, downpipes, intake, etc.
When I worked at the dealer they started a 335d with no mufflers, no resonators, just the DPF. Still as quiet as can be. That DPF really is an exhaust restriction. And the only reason it is there is to meet the restrictions for what comes out of the exhaust.