### Godot version

4.1.1-stable

### System information

Windows 10

### Issue description

When the project loads in editor, all the settings defined in project settings will be loaded over the default values, but when running the game nearly 95% of them will be ignored resulting in just loading the default settings.

here it's just loading only 4 variables from project setting and i have added the fifth in this pull request https://github.com/godotengine/godot/pull/80151
![image](https://github.com/godotengine/godot/assets/53877170/926168a6-e6d3-4983-b59d-7fd202db681d)

GLuint vertex_array = 0;
		GLuint index_buffer = 0;
		int sdf_point_count = 0;
		int sdf_index_count = 0;
		GLuint sdf_vertex_buffer = 0;
		GLuint sdf_vertex_array = 0;
		GLuint sdf_index_buffer = 0;
		bool sdf_is_lines = false;
	};
	RID_Owner<OccluderPolygon> occluder_polygon_owner;
	void _update_shadow_atlas();
	struct {
		CanvasOcclusionShaderGLES3 shader;
		RID shader_version;
	} shadow_render;
	struct LightUniform {
		float matrix[8]; 
		float shadow_matrix[8]; 
		float color[4];
		uint8_t shadow_color[4];
		uint32_t flags; 
		float shadow_pixel_size;
		float height;
		float position[2];
		float shadow_z_far_inv;
		float shadow_y_ofs;
		float atlas_rect[4];
	};
public:
	enum {