just for the record:
I made it through the laser sci fi place, beat the 4 bosses and have the upward beam activated.
not sure f I should go there yet, since it screams "final end boss".
And in the sci fi place, there are at least 2 places where there are solid laser barriers with likely some secrets behind it.
not sure where else to go though, since I likely need another power. but I already have the 6 arrows unlocked.
The lasers you mentioned should be deactivated after the death of the 4th boss.
That door in the main menu is just a decoration. It's there to show that the player enters the mountain.
For the interactable map, it marks items that are still uncollected. After using it, you can open the map in the menu then hold ctrl and scroll the map with wasd (keyboard), or triangle and directional keys (controller) to see uncollected items denoted by question marks.