IMO my expereince with BMW dealers is hit and miss and its a tough one to call whether to go dealer or independant.
I will give you an example, when mine went in to have the pressure converters changed, some of the vacuum pipes (die to the heat) were soldered onto the pressure converters and in order to release them they had to splice the edge of the hose. Now if I had done this myself I would have replaced the new hose. But BMW decided to push back on the old hose with the spliced end - resulting in the hose popping off because the end is loose. When I got the car back as I knew what i was doing I checked and found the old hose with the ends spliced popped off the PC - I could have replaced the hose myself but took it back to the dealer to rectify and when i got home I took the covers off to make sure a new vac hose was fitted. Reason why this was done at a dealer as the car is under warranty
On the other hand when I took my car for another simple fix to my local independant, while he was looking around in the engine bay he noticed that I had fitted an extra jubilee clip onto a vac hose to the turbo and he mentioned he had seen it and questionned my reasoning as it was not normal for this. For me this was attention to detail to see he had noticed this.
As you say a vehicle check is just another way of a MOT, whether you want to pay extra £20 for BMW only you can decide but personally I would be going the other way