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If you do the Skinned Tapir quest right away, the butterflies die and moths start appearing. It also allows you to go to the Pond and follow the path, as the butterflies blocking your path are now dead. It leads to one of the more intense scenes in the Hinterlands and worth checking out at least once. It's likely tied to the missing kids, but you can't revisit the church to know for sure. 

I haven't found the bones to effect any progression, as it seems like helping the god puts their souls at ease more than the Christian burial ever could.

In my own playthrough where I focused all of my full attention in developing P and Storm's relationship, (1) I go to the tailor and (1.1) donate P's clothes to make new ones for Storm. After donating P's clothes, Storm's house would now be available to go to but for the story's sake and that it would leave a much more impact in the story, I don't do that yet. (2) I go to the park and (2.1)  let P spend time with Storm. (3) I then go to library and (3.1) let P read fictional books instead of the nonfictional ones since Storm is seen eyeing up the fictional books only to look away once (I think) P saw him doing so. (4) I then go to the archeological sight and (4.1) have diner. After that, (5) I go to Storm's house and talk with his mother. There would be no choice given to you in that location. Next and I think is the last one, (6) I go to the pond and (6.1) let P talk with Storm. There would be a change of dialogue once you thoroughly develop the two's relationship where (SPOILERS: If you focused all of your full attention in developing their relationship, Storm would see P as someone he can trust and tell the exact and true reason as to how he was drained in the pond. The true reason being that his own mother was the one that drowned him. If you haven't develop their relationship, he'll lie and instead say that it was just some bullies that did it.) I don't know the exact day for the hot springs event but if you develop their relationship before that happens, dialogues would change and more interaction between them would happen.

In that whole playthrough, no lore was discovered but let's face it, it was all worth it in the end having to see this relationship between one another develop into something much more cute and much more intimate.