No, the "R5" program is not a farce; it is alive and well and is now going under the name "High Performance Windows Volume Purchase Program".
Essentially, there is no particular glazing configuration required by the Fed (this is a Department of Energy Program), as long as the whole window thermal performance is 0.22 or lower for operable units, and 0.20 for fixed. While it's a good rule of thumb to say that U = 1/R, that's not really the case, as there are a variety of factors which determine the overall U value of a window or door.
That being said, there are a number of manufacturers who have tested and comply with the DOE's criteria. Due to window framing conductivity, overall IG space and spacer material, this U value can be met with anything from 1 lite of Low-e with Argon fill (in the case of Mathews Brothers Company), to 2 lites of Low-e with Krypton fill (as is the case with other manufacturers). Obviously, there will be a difference in cost between those two options.
The challenge for the builder/remodeler now is finding the best solution to the overall performance goal. Instead of asking, "How much is your triple glazed, double Low-e, Krypton filled unit?", the question now should be, "How much is your U 0.22 unit?" In other words, why pay extra to achieve the same performance?