Tuners say it is restrictive, yes. They also developed their tune with certain mods mounted. While in development, Tuners may have even swapped out to different intake and DP's just to be sure the tune has worked regardless what the consumer may have mounted. So, they want their shelf-tune to work for everyone and give you the consumer a list of tune requirements just so there are no issues for anyone. Most only state an intake and DP without the inclusion of size. This goes for shelf tunes...now, custom tunes you can put on whatever you want and go get tuned.
But any way, here we go, I read an article many years ago. One shop, Autobahn in Riverside CA, was doing stage 2 mods on a early MK5. They were doing the intake, turbo back, and tune and concluded the oem size for intake and exhaust were sufficient. Reason they came to their conclusion was; they put the car on the dyno after they tuned it...then again on the dyno after adding the intake, and finally on the dyno after adding the full exhaust. They did do a base run stock first to see the HP gains with the tune. Results were the HP gains after they added the tune did not increase with the addition of the intake or exhaust. Take from it what you will...but it did show the oem bits are not restrictive. My first GIAC tune said I needed an intake and DP...but I just ran it with a drop-in oem location filter and stock turboback. Others are going to argue this and I am aware other tunes have some proof out there that the stage-2 DP and intake did show some slight gains having those bits of hardware. But you go look at Purdy's Golf R running low 11sec 1/4's with a stock intake.