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Basically I think the idea behind keeping the T focused on transit in Boston and the surrounding area (yes as far as the cape and Worcester) and not involved in this is the differences in grant writing (at least from when MassDOT explained it). As a transit agency (including yes commuter rail) the MBTA primarily seeks federal funding through FTA capital investment grants that are highly competitive across multiple modes and MassDOT wanted to keep them focused on that - these grants aren’t a good fit for his project due to the competitiveness and FTA’s cost benefit requirements. FRA has separate grant programs for Amtrak and intercity passenger rail (CRISI etc) and has a different process which MassDOT has always handled in house. Plus they felt Amtrak was the proper vehicle for this (and Amtrak also provided some grant match funding for the CRISI grant.)