There is almost always a premium when you design a more "efficient" building. The problem is, what should be seen as a no brainer, is seen as too costly. Developers don't typically have a stake in the building beyond the first couple years when it has been sold off. So all the pay back to the up front premium is never realized by the guys who paid for it. The only thing they are likely to do right now, is to pay the small premium to get the building LEED certified, which in an urban area such as Boston is almost a gimme. The only reason to do that, is to make your building more marketable. The real premiums start when you begin to ramp up the efficiencies being designed.
Owners who are developing their own buildings have a bit more of a stake in the effiency of their building and are willing to consider added costs for efficiencies as long as they can realize a quick pay back. Some will accept 5-10 year paybacks, but others we have dealt with are looking for closer to 2 years.
You may be alluding to the latest developments in building information modeling which is supposed to take care of field coordination before it even happens, and ends up streamlining the project. I have seen this work. In fact we are buttoning up a new football stadium in MN about 2-3 months ahead of schedule, which to me is unprecedented. This may in fact be due to the 3D modeling and clash reports generated before actual installation.
This however was not done by some brilliant architect, but by the GC. They probably used the architects Revit model, so he was a part of it too.