Good article. I am not going to touch the issue of why the freight railroads proceeded the way they did since there are some around here who get into an emotional hissy-fit about it, no matter what is said.
The reason all this was done as an overlay rather than a greenfield installation of a new system is that no one could figure out how to flashcut things over from one system to another without causing immense dislocation.
Under ideal circumstances it would have been ideally better to replace the PRR cab signalling system with either TVM-430 which was tried and tested system in the late 90s. The penalty that we pay is that the system is slightly more conservative and hence slightly less efficient since the PRR system provides only the status of the current section through the cab signal that is transmitted and there is no information about the actual status of the next section (i.e the signal that the train will be facing as it approaches the next section, except if it is a stop signal. Nor did it, before ACSES provide any distance to next target information, but that was mitigated through ACSES.