Just a couple of observations. I grew up in Flagstaff and there is a huge difference for those who live there and those who visit. The people who live there are just like everyone else. Flagstaff also has a huge transient population. I do not mean homeless, although there are those also. What I am taking about are those who stay there overnight or for a few days. They are both tourists and travelers. When I lived there, and I assume that it is the same still, the police would go through the hotel parking lots running tag numbers. They had an extraordinary high number of warrant arrests, car thieves and drug trafficker arrests due to that practice. The point is that while most tourists and locals are normal people there are some especially bad people that you can run into, especially at the hotels and certain other establishments that could give that "sketchy" vibe as described by a previous poster.
The father's report regarding the itinerary initially appeared useless because it is impossible to hike the Bright Angel Trail and visit Havasupai Village. A quick internet search provides a possible explanation for the confusing itinerary. The Wikipedia page for the Bright Angel Trail mentions that the Havasupai people created the upper part of the Bright Angel Trail when they would live part of the year at Garden Creek aka Indian Garden Campground.
The Bright Angel Trail hike from the rim to Indian Gardens and back in one day is very popular with tourists because it is just under 10 miles round trip, is an excellently maintained trail and if you are not staying over night no permit is required. Although never as a day trip, I have hiked the bright Angel Trail many times. Hiking down is quite easy but going back up can be difficult due to the 3000 ft elevation change. It would be even more difficult for someone from Louisiana due to the overall altitude. (the Rim is 6860 ft in elevation) Many people unaccustomed to the high altitude can underestimate the difficulty. Also, weather can be a concern. I have hiked that trail where it was in the 70's at Indian Gardens and snowing on the rim. More than once I have seen hikers suffering hypothermia on that trail because they felt warm while they were hiking but failed to realize how cold it had gotten. When they stopped for a break they either didn't have a coat or failed to put it on and their body temperature crashes in just a few minutes. Luckily, it is a heavily traveled trail and as was mentioned earlier, an excellently marked and maintained trail. Even if she had difficulty it is unlikely that she got off trail, or had a medical emergency that was not noticed by other hikers or park rangers.
My guess is that she underestimated how long the hike was going to take her. When she got back to the shuttle stop she was later than she had hoped and fearful that she may not make it back to Flagstaff on time. So either she mentioned that to someone or was simply doing what people do when they are late and waiting for a bus. (Kept checking the time and the schedule...looking down the road to see if it is coming...) Either way someone offered her a ride and she accepted.
Thinking about it, this would be a good spot for a predator, hike from the rim to the 1.6 mile resthouse, strike up casual conversation with the other hikers at the resthouse. Wait for someone who mentions or appears they are in a hurry. Hike the last 1.6 miles out with them, share some water if they are running low... Then once at the top and some rapport has been built they offer a ride. The earlier conversation on the trail makes them no longer seem like a stranger and the victim accepts the ride... It capitalizes on the fact that true hikers are very good people that are always willing to provide help to those they encounter in need. By posing as a fellow hiker it places the victim in a position of vulnerability because the predator is going to act in a way that is completely contrary to their past experience.
I doubt that she ever got back to Flagstaff. Her final text is the most telling, that it was not sent by her. "No, I am not going". That is just not what I would expect from a successful engineering student. Engineers are trained to communicate accurately. That means they state what is, not what is not. A statement of negation is too vague, it leaves too many possibilities to have acceptable accuracy in the engineering world. What I would expect would be I am late...changed plans...something that accurately describes what she is doing, not what she is not doing.