So, I beat the game (with all 11 lasers) but I still feel like I missed something. Yes, I know there are tons of "collectibles" to find all over the island, but there is an area or group of areas that are still out of my reach that I cannot seem to find an entrance into.

For example, the small building inside the town that seems related to crushing quarry rocks. There is a door next to the group of puzzles there that clearly leads down underneath the town. Or the hallway underneath the windmill. Instead of going down the hall towards the theater, to the left it seems to be another area that can be accessed on the other side.

The same problem can be found at the end of the sunlight temple. Right behind the elevator that raises the laser cannon here, there is another bared door that seems like it can be accessed on the other side. All the these underground areas, and I can't find an entrance into any of them. Has anybody else noticed this or figured out a way to get inside them?

Entering that area requires all 11 lasers; go poke around some more on top of/at the very depths of the mountain. Be sure to look at things from an angle you might not've had previously.

Nah, what you mainly need to do is to have a closer look at the box held by the statue on the top of the mountain, and then follow the yellow cable to where it leads. I don't think this is worth putting in spoiler tags since it's easy to miss and isn't really new a mechanic or an important revelation..