Finished BoF2, questions about some (unused?) areas. [FULL GAME SPOILERS]

I just beat BoF2 for the first time (I did get the good ending) and I'm wondering about some areas that I never ended up doing anything in. I'm wondering if I missed some secrets.

1. There's three "Huts" throughout the world map that I didn't find any purpose for. One is west of the Sea of Trees on a little peninsula, it has a cat in it. Another is west of Highfort down by the beach and has a generic male NPC who says something like "I don't have anything to do with it" or something. And there's a third I can't remember where but it was completely empty. Anything to do in these huts?

2. At the top of the right tower in Windia castle there's a room with flashing lighting coming through the windows and two NPCs who nervously say something like "haha, it's just flashing like that cause it's magic, everything is under control." I never did anything in that room. Did I miss something?

3. In Evrai in the entrance of the Grand Church there's three doors, the middle leading to the church proper and the left you come from later, but I never went in the right. It had bars blocking you from getting to a staircase. I never got down there. Actually there was also a nearly identical room in Windia, not the one that opens up to let you go down to get the Mark of the Bird, this one was on the opposite side of the castle. Was there any way to get to either of those?

I know I missed getting Boombada and I didn't get Seny early before Grand Church since I only learned about that today, so I know I definitely missed a few things. If anyone knows, let me know! Thanks!