I only discovered this near the end, but it’s something you can do from the start! I too thought they were stone circles, but they’re drain covers. Some of them can be… approached from above. Being vague in case you want to try to figure it out further, but glad to give more specific help if you want it.
The bell makes it nighttime. Most areas have something(s) altered, and it’s necessary to re-explore at night if you want 100%. There’s quite a lot more to do, if you’re so inclined. You can get the ghosts to follow you…
Yes, there’s another, but it’s way off down the road to 100%, IIRC.
Yes, the red glow means there’s more to do in that area. Not just collectibles.