Having read the entire report (thanks for the link), and without detracting anything from the obvious immediate root causes of the incident, I wonder if the report and root cause analysis do not dive deep enough into the recurring failures of the signaling system. In other words:
1) How often do signal system problems occur?
2) How often are trains required to be placed into "emergency bypass?"
3) Did (does?) the need to use "emergency bypass" on a relatively frequent basis lull the operators and associated staff into regarding "emergency bypass" as a more routine part of operations, as opposed to something very extraordinary that required extra considerations?
4) What is the frequency that other agencies use "emergency bypass" or similar workarounds? [And I'll acknowledge that this question is probably beyond the scope of the MBTA report, but perhaps something for the NTSB or FTA to chew on.]
What I don't see mentioned in the report is an acknowledgement that using the "emergency bypass" as a necessary workaround for signal system problems removes an important feature of positive train control. Operating the train in "emergency bypass" - even if the motorman had been following all the rules - introduces risks and increases the chances of an incident.
One of the recommendations of the report requires supervision when placing trains into "emergency bypass," so many of my above concerns are addressed. But the underlying crumbling infrastructure seems to be one of the causal factors for this incident that does not get enough attention in the report, although it does get a brief mention:
The Signals & Communications Department has appropriated funds to extend a signal trough from North Quincy to Braintree Station. This would replace the existing, aging data cables and provide a more robust signal without reliance on Verizon services.
While the communication and signal failures did not directly affect or contribute to the near miss unattended train incident; persistent and intermittent system failures do present an undesirable condition as they introduce abnormal operating conditions which may increase operational safety risks.
Again, not a big deal since the immediate root cause is so obvious, but food for thought, IMHO.