### 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].flags |= FLAGS_FLIP_V;
					}
					if (rect->flags & CANVAS_RECT_TRANSPOSE) {
						state.instance_data_array[r_index].flags |= FLAGS_TRANSPOSE_RECT;
					}
					if (rect->flags & CANVAS_RECT_CLIP_UV) {
						state.instance_data_array[r_index].flags |= FLAGS_CLIP_RECT_UV;
					}
				} else {
					dst_rect = Rect2(rect->rect.position, rect->rect.size);
					if (dst_rect.size.width < 0) {
						dst_rect.position.x += dst_rect.size.width;
						dst_rect.size.width *= -1;
					}
					if (dst_rect.size.height < 0) {
						dst_rect.position.y += dst_rect.size.height;
						dst_rect.size.height *= -1;
					}
					src_rect = Rect2(0, 0, 1, 1);
				}
				if (rect->flags & CANVAS_RECT_MSDF) {
					state.instance_data_array[r_index].flags |= FLAGS_USE_MSDF;
					state.instance_data_array[r_index].msdf[0] = rect->px_range; 
					state.instance_data_array[r_index].msdf[1] = rect->outline; 
					state.instance_data_array[r_index].msdf[2] = 0.f; 
					state.instance_data_array[r_index].msdf[3] = 0.f; 
				} else if (rect->flags & CANVAS_RECT_LCD) {
					state.instance_data_array[r_index].flags |= FLAGS_USE_LCD;
				}
				state.instance_data_array[r_index].modulation[0] = rect->modulate.r * base_color.r;