The 2.5" cat-back would without a doubt contribute to restrictions even on the 3.5“ downpipe as it wont flow enough. But the 3.5" will help drop the initial pressure at the downpipe but overall there will still remain slightly elevated pressure through out the majority of the system until reaching the twin pipe.
Launch Joel Racing released some nice data about back pressures with different size of exhaust configuration. Many exhausts for the MQB flow back down to 60mm which is a bit less then 2.5"....
Read Joels commenting bellow on this matter and see for yourself which is the best option.
Here you have three different back pressure CFD analysis of the MQB-platform.
3'' to 2.5'' Full 3'' 3.5'' to 2.5"
It is safe to say that the 3.5" down pipe has an overall worse backpressure through out the whole downpipe compared to full 3'' exhaust system.
All due to the large reduction of an whole inch drop which translates to a drop in roughly half the flow area.
But it has essentially the same backpressure as the full 3'' at the turbine housing outlet just that the full 3'' has an higher pressure in the first bend.
One more thing to take in to consideration when looking at all these colour scales and CFD analysis
is that in reality with a turbine and turbine housing the exhaust velocity
would be even higher, swirl effect from the turbine will also contribute to the backpressure.
Also if internal wastegate in use will disturb the swirl as the flows cross.
This means pressures can only get higher than this and should not be possible to drop below these ''perfect world results'' ever in the real world.
Follow Joel on Instagram for more CFD analysis @launchjoel_racing