Raton Line: Even in its day as the premium Chicago to LA train the Super Chief ran on the Raton Line. It bypassed Topeka KS, but otherwise followed the present day passenger route. Given that the ATSF at that time had 6 through trains and the Super was marketed primarily to high end through passengers, (It was an extra fare train) if there were advantages to the Amarillo Route for passenger trains, it would have gone that way. Kansas and Colorado both want the train on its present route. When New Mexico bought the piece of the line being used by their Santa Fe to Albuquerque commuter service the ATSF, or was it BNSF by that time?, was willing to sell all the remaining line north out of Albuquerque up to the Colorado state line for next to nothing, but that did not happen. I do not recall why.
Phoenix Line: Aside from being longer than the Clovis line through Maricopa, it is slower with numerous speed constraints in the portion east of Phoenix. I have a 2007 UPRR employee timetable for that area and calculated minimum run times therefrom. Emphasis on minimum. The real world times will be longer because there is no allowances for meets or any slack in these times. For the Phoenix line, I assumed that the entire length west of Phoenix itself would be brought up to Class 4 (80p/60f) standards and be given a 79 mph speed limit. For the line east of Phoenix, which is shown with a maximum speed limit of 60 mph for all trains, but a note that UP passenger trains are allowed 70 mph if there is no lesser (that 60 mph) limit in place, I assumed that 60 mph lengths could be 79 mph, 40 mph lengths could be 50 mph and all lesser limits could be at least 5 mph more than current limits. The Phoenix line times could be significantly understated, as in addition to the lack of any allowances for meets or slack in time, it is highly unlikely there would be zero less than 79 mph restrictions in the line west of Phoenix, plus some of the lower speed limits east of Phoenix could have to remain as-is and not all the 60 mph could be raised to 79 mph. These times do not include standing time at stops. Having said all this, I came up with Wellton to Picacho times of:
via Maricopa: 2 hours 15 minutes, averaging 73.8 mph over 165.9 miles
via Phoenix: 3 hours 8 minutes, averaging 66.8 mph over 208.9 miles
Thus, the time penalty would be 53 minutes, probably more.