I'm not that familiar with the legacy world, but my assumption is that the Keystone would operate on non-NEC rail as its own entity and then on the NEC up to NYP, it would operate with an NEC crew. It would be Amtrak all the way, but from a logistics and financial standpoint, it would be separated at the NEC.
I believe this was common in the "old days" and even today with the freights when it comes to trackage rights, etc. The Keystone should be paid for 100% by Pennsylvania and the state should receive 100% of the revenue, less a fee for trackage into NYP on the NEC and Amtrak reservations. Ideally, all the employees should probably be state employees... That's another flame war, though.
Actually, I do have a counter here: Amtrak owns the HAR-PHL line, so you could at least argue that the whole thing should "dump" to Amtrak. Ditto NHV-SPG, and now ALB-NYP. I'm not speaking to the vailidity of the argument, but it's at least there.
At present it looks like it is certain that ALB-NYP will be NY State responsibility in the PRIIA 209 sense. It is not clear exactly how NHV-SPG and PHL-HAR will pan out (at least to me), but I suspect some arrangement within the PRIIA regime will be worked out. I have not read PRIIA 209 in detail and I don't know how NHV-SPG and PHL-HAR is characterized in it.
My ESPA friends tell me that NYP-ALB is considered part of the Empire Corridor which is definitely seen as NY State responsibility and NY and Amtrak are working on an agreement that goes into force next year and NY State has budgeted money to cover the cost of current service and then some. There are sticking points in the negotiations involving things like food service which NY State wants restored between NYP and ALB on ALB terminators.
BTW, Amtrak does not own any of NYP-ALB. As far as I understand it (and it could be wrong) POU-SDY (actually Hoffmans) has been leased to NY State for 25 years (starting Nov 5 2012) with a possible extension of another 15 years, and NY State has chosen Amtrak to Maintain and Operate it for them (sort of like the NEC in MA except for the lease part). I am not very clear about how the lease payments are contracted to flow, but will find out at the next ESPA meeting. Of course Spuyten Duyvil - POU is owned by MNRR and Amtrak is a tenant, and NYP - Spuyten Duyvil is owned and operated by Amtrak. So NYP-ALB is not at all like the other two.