This has always been a bit of conundrum, especially when listing the Northern Tier + North Lakes Route since it has so many options. Many of the routes have alternates and spurs, some short and some long. Our basic rule is to list the main route number and you'll see that on the map cover. Alternates or spurs are not included in this number. On the longer alternates we will also list the alternate mileage on the cover. For example, Northern Tier section 5 is 227.5 miles from Fargo to Grand Rapids and the Little Falls Alternate is 256 miles. Only the 227.5 number is listed in the Cyclosource. When I add the mileages together using the main routes of the three different routes that make up Northern Tier + North Lakes Route it is 4,249 miles. And you listed several of the choices folks have on this routing.
So that is about 400 miles shorter than what is listed. To come up with the 4,651 number all the individually listed map section numbers were added together. In that 400 mile difference folks could add and subtract depending on whether they choose the main route or an alternate. So for this particular route it's easier for us to err on the side of caution with listing more miles.
We can qualify that number by saying "4,249 mi. main route" so on the next update of the Cyclosource we'll change the number.
Hope this explanation helps.