### 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)

};
	struct PolygonBuffers {
		GLuint vertex_buffer = 0;
		GLuint vertex_array = 0;
		GLuint index_buffer = 0;
		int count = 0;
		bool color_disabled = false;
		Color color;
	};
	struct {
		HashMap<PolygonID, PolygonBuffers> polygons;
		PolygonID last_id = 0;
	} polygon_buffers;
	RendererCanvasRender::PolygonID request_polygon(const Vector<int> &p_indices, const Vector<Point2> &p_points, const Vector<Color> &p_colors, const Vector<Point2> &p_uvs = Vector<Point2>(), const Vector<int> &p_bones = Vector<int>(), const Vector<float> &p_weights = Vector<float>()) override;
	void free_polygon(PolygonID p_polygon) override;
	struct InstanceData {
		float world[6];
		float color_texture_pixel_size[2];
		union {
			
			struct {
				float modulation[4];
				union {
					float msdf[4];
					float ninepatch_margins[4];
				};
				float dst_rect[4];
				float src_rect[4];
				float pad[2];
			};