Peace Talks is a whodunnit as regards Thomas, you don’t get much of a beginning because it spoils the reveal. The majority of what’s left is a beginning of the Peace Talks setup and part of the middle for both the Thomas and the PT plots. I think that it was cut prematurely, they should have had his return to Chicago and perhaps half a dozen further chapters, but it was cut at this point because the first couple of chapters of BG contain a huge surprise for the reader, which if we have guessed isn’t going to be a surprise. So mutilation for nothing.
The problem is that a whodunnit is supposed to be a setup for a scene where our intrepid detective sits all the suspects down in the library and expounds his "Here's what happened..." complete with twists and reveals and the culprit making a break for the exit, before being hauled off to justice in an undignified manner.
We got a beautiful version of this at the end of Turn Coat.
Not so much with Peace Talks -- we still don't know who dunnit.
Thomas being "safe" in the prison isn't even a satisfying release of the mild "Is Thomas going to die?" tension, since we still don't know how far gone he is or if it will be possible to save him outside the cell.
But, I agree that it's structural issues from cutting the book. I wish they'd published "Peace Talks, Part I" and not worried so much about trying to make one sort-of-but-not-really resolved plot arc in the first book.