A few years ago I applied for an engineer position at Keolis, and was hired. Unfortunately so family trouble precluded me from accepting. In the process, I learned some things which should answer some of the questions. First, only the top few managers stay with Keolis. Everyone else stays, not matter what. That is why some employees are still employed through the long list of contractors. Many started with B&M, and continued through Amtrak, MBCR, and finally Keolis. As far as pensions go, the vast majority are covered under RRB. Maybe managers have an additional company pension.
I'm in agreement with other posters about the $h!t sandwich which Keolis was given. I think that if a contractor was unscrupulous they could easily pull the wool over the eyes of the Mass DOT people, who likely have no railroad experience. The problem is that most railroaders of today are brainwashed to the ways of the late Hunter Harrison. It would be very difficult to find a railroader like of Dusty.
The last point is about the equipment. It seems like since many o the commuter agencies have gone public sector, the equipment is getting stranger and stranger. Every new contract seems to be like reinventing the wheel. In this regard, I applaud Metra. They have stuck to the same basic gallery car as has been used for the last 60 years. Their power is generally old, but the new units are still mostly bulletproof EMD products. Even the MPI units are mostly built around proven EMD designs. Maybe other agencies need to take note.