Sorry Mike but I don't understand the different purposes of the two plans. Which is more advanced?
the 39 weeks is ending with 4 weeks tapering while the 36wks with only 2: why?
The plans were both designed in the same way, with principles of periodization and mixing up the focus among the three sports. The reason they are different lengths is nothing significant, just due to the fact that they were laid out initially with different target races in mind.
As for the different lengths of the tapers, there's a basic need to be more rested & sharper for a shorter race, where seconds matter, than with a longer ultra race. Prior to an Ironman I want to be rested, but still have a bulk of my aerobic conditioning at a peak.