### 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)

MAX_RENDER_ITEMS = 256 * 1024,
		MAX_LIGHT_TEXTURES = 1024,
		MAX_LIGHTS_PER_ITEM = 16,
		DEFAULT_MAX_LIGHTS_PER_RENDER = 256,
	};
	
	
	
	struct CanvasLight {
		RID texture;
		struct {
			bool enabled = false;
			float z_far;
			float y_offset;
			Transform2D directional_xform;
		} shadow;
	};
	RID_Owner<CanvasLight> canvas_light_owner;
	struct OccluderPolygon {
		RS::CanvasOccluderPolygonCullMode cull_mode = RS::CANVAS_OCCLUDER_POLYGON_CULL_DISABLED;
		int line_point_count = 0;
		GLuint vertex_buffer = 0;