I got in touch with the author of the story on Twitter, and he clarified that the current contract, which wasn't uploaded by WNPR on the website for some reason, simply incorporates the previous contract by reference and then mentions changes to the terms of the contract from the previous version, and that the amendments listed for the current contact do not contain the "one ticket, any train" clause that Connecticut has said it does. (the two links collectively contain the full exchange).
See section 3(b). To really know what's going on with the ticketing, we need to know every tarriff proposal which has been sent by CDOT to Amtrak, and which ones Amtrak responded to (since non-response is considered acceptance). That's one heck of a weird clause. If CDOT proposed an "all tickets are equal" tarriff and Amtrak accepted it, CDOT is on solid ground.
3(d), which Amtrak is leaning on when claiming "safety" concerns, is also phrased really weirdly, and I would have trouble interpreting its legal meaning. First it says that Amtrak may unliaterally make changes which are necessary for safety, environmental, operational, or legal reasons. Then it says "Amtrak and the states agree that said changes shall result from temporary and/or emergency conditions." Which is a really weird way of putting it. Does it mean that Amtrak can only do this for temporary/emergency conditions, or does it mean that the States stipulate that they will treat any such action as if it resulted from temporary/emergency conditions?
Section 1(c) seems to be the one where CDOT can request assignment of additional equipment or service (or less), and Amtrak is required to tell CDOT whether that is feasible, how much it will cost and when they can implement it. We don't know whether this has been invoked.
Section 1(d) fixes the consist sizes to what they were in 2014 (as noted in appendix I A), unless the States and Amtrak agree to change it. I don't know which trains are the overfull trains, but it would be interesting to compare that with the required 2014-era consists. It *also* says that if the trains are full, the state can ask Amtrak to assign more equipment and
Amtrak shall endeavor to provide additional rail passenger serivce equipment from its available resources commensurate with the funding requirements of the Agreed 209 Methodology
I take this to mean that if the trains are full and CT requests longer consists, Amtrak *must* find the extra equipment, provided CT pays for it according to the standard "209" pricing. (I.e., if the train is full and CT pays for more cars, they have to take that equipment away from the NEC -- no choice.)
Anyway, this gives more information, but absolutely does not give enough information to tell what the situation between CT and Amtrak actually is. We don't know which clauses CT has invoked or whether they have made the offer to pay for additional cars; we don't know what the active tarriff agreements between CT and Amtrak are; we don't even know what's in the renewed/modified contract.
There are definitely clauses in here which could put CT 100% in the right and Amtrak 100% in the wrong... or vice versa. Depending on which of these clauses has been invoked so far, and in what manner.