You see as you study the history of our nation, you will find that over and over again their are very few routes cut direct from the wilderness, and most tend to be built and rebuilt on, or near each other over and over. The National Old Trails Road itself essentially followed pre-existing trails from the pioneer era such as the Santa Fe Trail, and the National Road.
The Santa Fe Railway does not follow the National Old Trail directly, since its main routes like those of the California Limited and later the Super Chief started their westward trek in Chicago. These trains would finally catch up with the National Old Trail near Kansas City, MO and follow it closely to Los Angeles.
Route 66 travels the National Old Trail in a both direct and indirect way. Route 66 like the Santa Fe's premier passenger liners started its westward trip in Chicago. For the most part Route 66 and the Santa Fe crisscross each other between Cicero and Joliet, IL, when the finally go their separate directions meeting up again in Las Vegas, NM or Albuquerque, NM depending on the alignment of Route 66 at the time.
Route 66 catches up with the National
Old Trail in St. Louis, MO. However, a Route 66 breaks southwest after St. Louis, as to where the National Old Trail continues west. Route 66 meets up again with the National Old Trail in either Las Vegas, NM or Albuquerque, NM, the the latter indicating one of the later alignments of Route 66 in which Las Vegas, and Santa Fe, NM where bypassed.
The National Old Trail and Santa Fe Trail basically served as templates for both the Santa Fe Railway, and Route 66. Part of the reason is because this southern route allows travel from the Easts last big city to the west coast through terrain that is devoid of the mountainous terrain found further north, terrain that was taxing on locomotives, cars, and particularly travelers.
If you study old trails you will find this type of planning common. Look at the way the Mormon Trail, Oregon Trail,Transcontinental Railway route, Lincoln Highway, US 30, and now modern I-80 all follow along the same basic path and terrain. This is a perfect example of how terrain and primitive trails can dictate travel, and interstate commerce, as is what we see with the routes predating Route 66, and Santa Fe.