### 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)

state.instance_data_array[r_index].color_texture_pixel_size[0] = texpixel_size.x;
				state.instance_data_array[r_index].color_texture_pixel_size[1] = texpixel_size.y;
			} break;
			case Item::Command::TYPE_POLYGON: {
				const Item::CommandPolygon *polygon = static_cast<const Item::CommandPolygon *>(c);
				
				_new_batch(r_batch_broken);
				state.canvas_instance_batches[state.current_batch_index].tex = polygon->texture;
				state.canvas_instance_batches[state.current_batch_index].command_type = Item::Command::TYPE_POLYGON;
				state.canvas_instance_batches[state.current_batch_index].command = c;
				state.canvas_instance_batches[state.current_batch_index].shader_variant = CanvasShaderGLES3::MODE_ATTRIBUTES;
				_prepare_canvas_texture(polygon->texture, state.canvas_instance_batches[state.current_batch_index].filter, state.canvas_instance_batches[state.current_batch_index].repeat, r_index, texpixel_size);
				state.instance_data_array[r_index].modulation[0] = base_color.r;
				state.instance_data_array[r_index].modulation[1] = base_color.g;
				state.instance_data_array[r_index].modulation[2] = base_color.b;
				state.instance_data_array[r_index].modulation[3] = base_color.a;
				for (int j = 0; j < 4; j++) {
					state.instance_data_array[r_index].src_rect[j] = 0;
					state.instance_data_array[r_index].dst_rect[j] = 0;
					state.instance_data_array[r_index].ninepatch_margins[j] = 0;
				}
				_add_to_batch(r_index, r_batch_broken);
			} break;
			case Item::Command::TYPE_PRIMITIVE: {
				const Item::CommandPrimitive *primitive = static_cast<const Item::CommandPrimitive *>(c);
				if (primitive->point_count != state.canvas_instance_batches[state.current_batch_index].primitive_points || state.canvas_instance_batches[state.current_batch_index].command_type != Item::Command::TYPE_PRIMITIVE) {
					_new_batch(r_batch_broken);
					state.canvas_instance_batches[state.current_batch_index].tex = primitive->texture;
					state.canvas_instance_batches[state.current_batch_index].primitive_points = primitive->point_count;
					state.canvas_instance_batches[state.current_batch_index].command_type = Item::Command::TYPE_PRIMITIVE;