I keep going back and forth on this myself. Contrary to my relatively harsh statement above, I think you make a valid point here. I won't say "99% of people won't notice this," probably it's a lower percentage. But it's not trivial. I'd amend my earlier harshness by saying that people who buy the SB2 for gaming will notice it. IF it doesn't affect creative apps (e.g., the Sketchup and CET apps that my wife runs, that depend on a fast GPU for decent performance), then it won't matter to the SB2's key constituency.
So, the challenge for Microsoft will be to describe this to people in a way that doesn't oversell it as a hardcore gaming system and at the same time doesn't undersell it as a powerful machine for creative types. I think they're okay relative to their MacBook Pro positioning, because even if you throttle the GTX 1060 it's still going to be faster than the AMD GPU in the Apple machine.
I'm likely going to go ahead and pick one up, particularly given the holiday return period. I'll have plenty of time to work the machine out before need to make a final decision. I'm guessing it'll be more than fine for my own needs -- I'm not much of a gamer so I won't run into that particular issue myself