It seems like PTC is a bigger issue than PPC at this point. Maybe it was a typo.
No, it wasn't. It isn't the withdrawal of the PPCs that caused the heartburn in question, it's the fact that (for example) Amtrak mucked about with the wine and cheese tastings (which were rather a promotional item for the states in question) without reaching out. To be fair, though, both incidents (alongside the whole station agent mess) are pretty good cases of Amtrak handling things clumsily.
On overhead: You have two-and-a-half issues there. The first is that there's rather a decent case that the NEC should be carrying more of the overhead, with the half-issue being an argument that a chunk of the overhead should be getting billed to the federal government as part of Amtrak's appropriation and handled as an explicitly non-allocated cost. Bear in mind that, for example, the presence (or absence) of Sunnyside or Ivy City has close to zero impact on California. The fact that the switch from "avoidable costs" to "fully allocated costs" in the 1990s led to a one-year 65% jump in expenses is a pretty good sign, in my mind, that Amtrak probably got a little too aggressive here (though indeed, some of this may have also been a result of Amtrak losing the Pioneer/Desert Wind). It doesn't help that in many respects, Amtrak allocates a lot of expenses as "overhead" when a good portion of those expenses could (and probably
should) be handled as directly billed items. A good example here is advertising (which is billed to a given state even if Amtrak doesn't spend anything on advertising in that state and the state's DOT does their own advertising work).
The second, and probably bigger, issue is that a loss of overhead control (or perhaps a lack of it to begin with, if only due to the origins of Amtrak) is a
very good way to end up losing contracts. NB Amtrak didn't get the Hartford Line contract for reasons related to this (and then, I'm told, tried to strongarm CT over access to the line only to be reminded that CDOT/MNRR owns New Haven to New Rochelle).
And I think there's a clear difference between fighting over details on a major infrastructure project and continuing issues with the status of a contract. The sense I've gotten, and numerous incidents have reinforced this, is that Amtrak is happy to take quite a bit for granted.
Edit: To be clear, I think what you're ultimately seeing with various states is a "death by a thousand cuts" in terms of what Amtrak is doing to itself. It isn't one big, gigantic frak-up...it's an extended pattern of behaviour that makes it apparent to the states that Amtrak doesn't really care about their business becuse hey, who can they turn to? And in many cases, this behavior has been going on for a long,
long time.