Personally I think this is great! Amtrak and NJTransit should have been working together from the get go. I think this goes to show the Governor of NJ was right to do what he did.
The money's got to come from somewhere and the tunnel will directly benefit NJ as soon as it's finished. So Christie was "right" to pass the cost of that investment off onto a federal agency that's in an even more tenuous financial situation than NJ?
Christie did what he did because (a) the NJT bureaucracy was less than forthright in stating the actual cost of the project and was trying to toge tit going so that when they ran out of money it would be a fait acompli and NJT tax payers would be stuck with a bad situation.
In any event all along it was and still is a good idea for NJT and Amtrak to work together on a project that works well for both. If $15 billion is going to be spent might as well do it so that the most are benefited in the region and on the NEC. NJT spending off $12 billion on a tunnel that benefits only itself is not the best use of that money, and it would have made it more difficult to find additional money to do the needful for improving connectivity into Penn Station to benefit the region as opposed to just NJ.
People who are thinking that another pot of money could be found for Amtrak to build its own tunnels to Penn Station by 2030 after NJT had managed to finish its own Big Dig over budget and behind schedule, are just kidding themselves.
The source of funding any project that happens eventually will be a combination of federal, state and PA, so no one is pushing any funding off to anyone else. Too early to even know what the mix is going to be. Just because Amtrak is involved does not mean all funding will be federal. Indeed considerable amount of the interlocking improvements in NJ on the NEC is funded by NJ and not the federal government.
Finally the Feds in principle are never in a more tenuous financial situation than a state at least as far as cash flow is concerned. A state cannot print money. The feds can.
Not that it is a good idea for them to do so endlessly, but as a matter of law they can. The states cannot.