Before we get off track please everyone note that SI is not to determine the hardest hole it but to identify the hole that gives the scratch player the largest advantage. Obviously par 5's are most likely the lowest SI because scratch players can two putt for birdie. The 17th at St. Andrews is fairly the #5 hole because everyone plays it poorly and not just because of length.
As someone who has actually recommended the stroke index ratings for a lot of courses [I've suggested it for about 25 of my own], I can say there is certainly not a universally accepted way of doing it.The USGA recommends collecting scorecards from low handicappers and mid-to-high handicappers and assigning strokes according to the differential between the two groups. At Stonewall (Old), this resulted in a short, tight par 4 [the 4th hole], where low handicappers hit an iron off the tee and high handicappers make X hitting driver, becoming the #1 handicap hole. Getting a stroke generally doesn't help when you are making X. So I'm not a big fan of the official system.
As for architecture, I have long been resistant to the idea that the hardest hole should be at the end of the round, as many American designers seem to believe. There are plenty of examples to the contrary, not only in the UK [where match play mentality dominated early design] but also in the U.S. [Pine Valley, Pebble Beach, Augusta, Shinnecock, National, Cypress Point, etc.].