Nidal: their borders should have been closed anyway, and any major dealings are made with the Umbral Court, not easy with closed borders and and heretical cult.
True enough. It ended up not being a feature at my table, as my party was uninterested in venturing into Nidal, and quite nervous about them throughout. The fact that Nidal doubled their forces on the Southern border in book 1 made it more logical that they would send a diplomatic delegation to Ravounel to ensure peace or, better yet, a mutual defense pact.
Alignments: depend if they talked before or after their actions, and good rolls should not help with alignment shifts, the rolls help with normal people, nor reality itself or the gods.
The goal of the AP is to change the world. NPCs' alignments changing is a feature not a bug. As for the PCs, which were in the NG/CG range except for the monk, their alignments weren't going to change because of this. The Monk made sure that they had reported what they were doing to the lawful authority in charge of defense policy, the Mayor, who was true Neutral. During the questioning, however, the player was definitely playing his alignment straight, trying to navigate a lot of moral quandaries. And that's the important thing, really.
for the rest, they might still have to deal with a certain Thrune, not sure if they will be welcomed in Hell.
We're not doing the sojourn in Hell part, but they will have one last fight with that Thrune. The AP will end where it started, in Kintargo.