I can't speak to train 59, but I just took #90 from NY to Savannah. The schedule was depart Penn at 6:05am and arrive in Savannah at 9:03pm. We had about half an hour of freight delays and another 45 minutes due to an emergency brake trip (or some other unexplained sudden stop we encountered), but we still got into Savannah by 9:15. I assume there were about an hours worth of expected delays padded into the schedule, it turned out to work perfectly sans ten minutes.
What is interesting is that 89 and 90 probably has the tightest schedule of all the LD trains (LD as in more than 750 miles Amtrak system trains).
Checking Amtrak Status Maps Archive Database tool, the #89 Palmetto has gotten into SAV early 7 times out of 37 trips since August 1. And over an hour late 7 times, so the padding gets used most trips.
The database tool is quite useful as I used it to display all the arrival times for #89 into SAV for a month. I then looked up the individual trips that were more than a little late, > 45 minutes for the Palmetto, in the Status Map Archives. I then did it for the month of May. The pattern jumps out: when the southbound Palmetto gets into SAV late, it is almost always due to delays encountered between Alexandria and Rocky Mount. This came up in a recent discussion, but improve that segment - which will see some improvements in the coming years from HSIPR grants and VA funds - Amtrak could take padding out for the Palmetto, the Silvers, and the Carolinian.