MBTA owns the ROW from state line to Boston and obviously does everything related to the stations Amtrak doesn't share. But Amtrak is the dispatcher and track maintainer for the whole line, and each party's future improvements bucket list is jointly co-signed on the NEC Improvements Master Plan.
The two parties are generally sympatico with each other's aims, but technically Amtrak is the one in day-to-day control of it. Think of the T's role on the Massachusetts NEC as more "Chairman of the Board" and Amtrak's the "CEO"...the T's intimately involved in approving every executive decision, but Amtrak's the one making the hands-on calls.
On the greater-NEC route network they have ownership and control New Rochelle to D.C., New Haven to the MA state, Keystone Corridor, Empire Connection, and Springfield Line. They have no ownership but do have control for the MA NEC and Hudson Line from Poughkeepsie to Albany. They have neither ownership nor control on MNRR New Haven Line, MNRR Hudson Line south of Poughkeepsie, and south of the D.C. Union tunnel portal where the Virginia NE Regionals spit out onto CSX track the rest of the way.
