I get that RR's have to build in SOME extra time. And I accept that (hadn't heard that claim before). I do think that there are problems with this amazingly old schedule - some easier to fix than others. Like I've no idea why that one EB train would pull out of HP every single night and then sit for 15 to 20 minutes. To me that seems like really bad scheduling. Reminds me of someone in MTA when they still ran buses in Nassau, who for decades made sure that a certain bus route (to NorthShore University Hospital) always pulled out of the LIRR station in question a minute or two BEFORE an EB train would arrive, creating a 30 to 60 minute wait for the next bus. At the time, I had a baby there in NICU and I would leave work every afternoon, head out to see him and be with my wife, and that scheduling made it much harder and more painful. Some time later, that MTA scheduling manager retired, and his replacement fixed the schedule.
Many times I would be at Penn, with two trains heading towards Great Neck leaving minutes apart every single day, with another one or two a short time later, etc. Those of us waiting for PJ or Huntington trains, especially PJ, had much longer waits. Plus, the GN trains were usually half empty at best most nights, while we had to squeeze. Same sort of thing with lots of South Shore trains, often far less than full.
I did eventually learn one reason PJ service has long been so poor. A certain retired on the job LIRR president told me, face to face at a public meeting, that only farmers lived east of Huntington, so no more service was needed. And how often did you need to transport their milk and farm goods to the west?