### 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)

ERR_FAIL_INDEX_V(p_layer_id, physics.size(), Vector<Vector2>());
	ERR_FAIL_INDEX_V(p_polygon_index, physics[p_layer_id].polygons.size(), Vector<Vector2>());
	return physics[p_layer_id].polygons[p_polygon_index].polygon;
}
void TileData::set_collision_polygon_one_way(int p_layer_id, int p_polygon_index, bool p_one_way) {
	ERR_FAIL_INDEX(p_layer_id, physics.size());
	ERR_FAIL_INDEX(p_polygon_index, physics[p_layer_id].polygons.size());
	physics.write[p_layer_id].polygons.write[p_polygon_index].one_way = p_one_way;
	emit_signal(SNAME("changed"));
}
bool TileData::is_collision_polygon_one_way(int p_layer_id, int p_polygon_index) const {
	ERR_FAIL_INDEX_V(p_layer_id, physics.size(), false);
	ERR_FAIL_INDEX_V(p_polygon_index, physics[p_layer_id].polygons.size(), false);
	return physics[p_layer_id].polygons[p_polygon_index].one_way;
}
void TileData::set_collision_polygon_one_way_margin(int p_layer_id, int p_polygon_index, float p_one_way_margin) {
	ERR_FAIL_INDEX(p_layer_id, physics.size());
	ERR_FAIL_INDEX(p_polygon_index, physics[p_layer_id].polygons.size());
	physics.write[p_layer_id].polygons.write[p_polygon_index].one_way_margin = p_one_way_margin;
	emit_signal(SNAME("changed"));
}
float TileData::get_collision_polygon_one_way_margin(int p_layer_id, int p_polygon_index) const {
	ERR_FAIL_INDEX_V(p_layer_id, physics.size(), 0.0);
	ERR_FAIL_INDEX_V(p_polygon_index, physics[p_layer_id].polygons.size(), 0.0);
	return physics[p_layer_id].polygons[p_polygon_index].one_way_margin;
}
int TileData::get_collision_polygon_shapes_count(int p_layer_id, int p_polygon_index) const {