It occurs to me that perhaps you have not double checked that the normals on your mesh are properly aligned and that those dark vertices are pointing the wrong way.
In Blender (or your 3D editor of choice), select all vertices and use “recalculate normals” to fix this, then reimport the mesh.
I recalculated the normal in blender and it didn’t work . I tried changing the light map texel size to 1x while importing the mesh in godot and it fixed the issue. But it created another issue as you can see in the screenshot.
I am not sure what is going on exactly, but setting the quality higher gets rid of the noise, so clearly part of the problem is you’re baking a massive area to a single texture. But that’s not all, because your blender files have procedural walls, I assume you imported those directly, which means you did not unwrap the UVMap yourself, which means the UVs are whatever size godot guessed. If you look at the texture the bake makes you can see the illuminated area is tiny and there’s a lot of black. With custom UVs you’d get more detail where it matters. But that’s not all. Because the inner corners of your geometry are not actually connected AND the texture space is so limited, the edges that are in the shadow cause a gradient to show.
Basically, you need to be more careful and make better models if you want to have pretty shadows. As far as I can tell, those are the issues here. All in the way the meshes are created, not in the baking or importing.
Even if you do that, you definitely have to fix the vertices that are inside or behind another volume, since that’s the main cause of the wrong shadows, even tho some of them will disappear into the geometry with better UVs.