Okay, here is my thinking on that. The outlet of the turbine (the exit of the turbine wheel) is right around 2.5" in diameter. The distance from the exducer of the turbine wheel to the flange surface is about 1 inch or so. Technically, here we have a 2.5" "pipe" that is about an inch long. Let's install a 3" downpipe now. If your reasoning is correct, then we still have a "restriction" in the exhaust. The restriction is in the turbo itself and not in the downpipe.
I was thinking that the 12" section of 2.5" pipe I want to use is simply an extension of the turbine outlet. If this is not correct, then ideally you would want the turbine outlet to be 3" as well. I have never seen an outlet that big on a street turbo.
How about this: Dyno a car with a 2.5" downpipe and 3" exhaust. Dyno the same car with a 3" downpipe and 3" exhaust. The setup with the 3" downpipe would produce more power, wouldn't it? That's because the 2.5" "restriction" is only as long as the downpipe.
I think that the shorter the restriction is, the less power you will lose.
P.S. I am not looking forward to bashing in the dents for the bolts

But, in the name of having a 3" downpipe, it is worth it!
Thanks for your advice,