If Thomson were alive in the mid 20th century he would have had diesel powered, hydraulically actuated earth moving equipment and trucks plus dynamite to build a a right of way over the Allegheny frontal.
The ideal heavy freight railroad in America is one with a gradient of 1 per cent or less. No extra power is needed assuming that curvature does not contribute to the friction of a moving train.
This exercise is using the existing Pittsburgh to Harrisburg as much as possible. Suppose a line is drawn from the vicinity of Cresson at milepost 250 to the vicinity of Tyrone, PA near milepost 222. The line is 22 miles in length. The existing railroad is 28 miles in length.
A straight line northeasterly from Cresson to Tyrone crosses largely undeveloped forest, some farmland and very little developed space. Yes, some large fills and cuts would be required but no more so than a typical right of way for an interstate highway crossing the Alleghenies.
The elevation at Tyrone is close to 900 feet. The elevation at Cresson is 2030 feet. For simplicity, 2000 feet minus 900 feet means that 1100 feet in elevation must be overcome. That would be 50 feet elevation for each of the 22 miles. That equates to 0.9 (nine tenths) of 1 per cent gradient. The line would be just less than a 1 per cent grade. It would be capable of 110 mph operation.
Assuming the operation of a passenger train at its maximum allowable speed for the 28 miles, The current line has a maximum 51.9 mph operational limit requiring 32.66 minutes. That is an ideal speed estimate not accounting for a station stop.
In comparison, the suggested 22 mile new line operated at a conservative 90 mph would require 14.6 minutes. That would be an 18 minute time saving.