### Godot version

4.01

### System information

Windows 10

### Issue description

It seems a tiles Custom Data is cleared/not set when "Local to Scene" is enabled for the TileMap in the Resource section. At least the custom data isn't set by the time of the _ready function in the script attached to the TileMap.

### Steps to reproduce

create TileMap and tileset with custom data and attached script. in _ready method attempt to read custom data from a used cell. 

In Attached project run it. It will print_debug if it found custom data or not. "Local to Scene" is enabled so it will not find the custom data.

### Minimal reproduction project

[TileMapCustomDataLocalBugReproduce.zip](https://github.com/godotengine/godot/files/11470771/TileMapCustomDataLocalBugReproduce.zip)

property_info = PropertyInfo(Variant::OBJECT, vformat("navigation_layer_%d/%s", i, PNAME("polygon")), PROPERTY_HINT_RESOURCE_TYPE, "NavigationPolygon", PROPERTY_USAGE_DEFAULT);
			if (!navigation[i].is_valid()) {
				property_info.usage ^= PROPERTY_USAGE_STORAGE;
			}
			p_list->push_back(property_info);
		}
		
		p_list->push_back(PropertyInfo(Variant::NIL, GNAME("Custom Data", "custom_data_"), PROPERTY_HINT_NONE, "custom_data_", PROPERTY_USAGE_GROUP));
		for (int i = 0; i < custom_data.size(); i++) {
			Variant default_val;
			Callable::CallError error;
			Variant::construct(custom_data[i].get_type(), default_val, nullptr, 0, error);
			property_info = PropertyInfo(tile_set->get_custom_data_layer_type(i), vformat("custom_data_%d", i), PROPERTY_HINT_NONE, String(), PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_NIL_IS_VARIANT);
			if (custom_data[i] == default_val) {
				property_info.usage ^= PROPERTY_USAGE_STORAGE;
			}
			p_list->push_back(property_info);
		}
	}
}
void TileData::_bind_methods() {
	
	ClassDB::bind_method(D_METHOD("set_flip_h", "flip_h"), &TileData::set_flip_h);
	ClassDB::bind_method(D_METHOD("get_flip_h"), &TileData::get_flip_h);
	ClassDB::bind_method(D_METHOD("set_flip_v", "flip_v"), &TileData::set_flip_v);
	ClassDB::bind_method(D_METHOD("get_flip_v"), &TileData::get_flip_v);
	ClassDB::bind_method(D_METHOD("set_transpose", "transpose"), &TileData::set_transpose);
	ClassDB::bind_method(D_METHOD("get_transpose"), &TileData::get_transpose);
	ClassDB::bind_method(D_METHOD("set_material", "material"), &TileData::set_material);
	ClassDB::bind_method(D_METHOD("get_material"), &TileData::get_material);