For one principal reason, typing as someone who can only guess at the PAR decision-making process, I can think why they would want to keep things inefficient and costly on branches: getting a favorable exemption decision from STB on as many branches as possible. Fewer branch customers reduce power, fuel, crew, and maintenance requirements. Check the thread on the Watertown Branch.
By demonstrating a high cost of service, PAR or any other line, for that matter, can build a case for exemption. One e long-term consideration is the increasing number of 286K cars. Track that was originally built for 220K or even less and is already 10 MPH would have to be rebuilt from roadbed up to deal with the extra stresses of heavier loads. The number of 263K cars will decrease in the future, making branch lines even more desirable candidates for embargoing and exemption applications.
As background for the above, a few years back, Trains magazine had an article that mentioned statisitician W. Edwards Deming, generally credited as the formulator of Total Quality Management and the person who helped turn the phrase "Made in Japan" into a positive instead of a negative. While at the University of Iowa, Deming was commisioned by a midwest railroad to prove that passenger trains were money-losers. This was before Interstates and passenger jets, but Deming came up with research that proved his customer's case.
Even with 2-man crews, lines make their real money with bridge traffic, not local, especially not branch local traffic, unless it is high-volume.
"A gray crossover is definitely not company transportation."