### 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)

ClassDB::bind_method(D_METHOD("set_terrain_peering_bit", "peering_bit", "terrain"), &TileData::set_terrain_peering_bit);
	ClassDB::bind_method(D_METHOD("get_terrain_peering_bit", "peering_bit"), &TileData::get_terrain_peering_bit);
	
	ClassDB::bind_method(D_METHOD("set_navigation_polygon", "layer_id", "navigation_polygon"), &TileData::set_navigation_polygon);
	ClassDB::bind_method(D_METHOD("get_navigation_polygon", "layer_id"), &TileData::get_navigation_polygon);
	
	ClassDB::bind_method(D_METHOD("set_probability", "probability"), &TileData::set_probability);
	ClassDB::bind_method(D_METHOD("get_probability"), &TileData::get_probability);
	
	ClassDB::bind_method(D_METHOD("set_custom_data", "layer_name", "value"), &TileData::set_custom_data);
	ClassDB::bind_method(D_METHOD("get_custom_data", "layer_name"), &TileData::get_custom_data);
	ClassDB::bind_method(D_METHOD("set_custom_data_by_layer_id", "layer_id", "value"), &TileData::set_custom_data_by_layer_id);
	ClassDB::bind_method(D_METHOD("get_custom_data_by_layer_id", "layer_id"), &TileData::get_custom_data_by_layer_id);
	ADD_GROUP("Rendering", "");
	ADD_PROPERTY(PropertyInfo(Variant::BOOL, "flip_h"), "set_flip_h", "get_flip_h");
	ADD_PROPERTY(PropertyInfo(Variant::BOOL, "flip_v"), "set_flip_v", "get_flip_v");
	ADD_PROPERTY(PropertyInfo(Variant::BOOL, "transpose"), "set_transpose", "get_transpose");
	ADD_PROPERTY(PropertyInfo(Variant::VECTOR2I, "texture_origin", PROPERTY_HINT_NONE, "suffix:px"), "set_texture_origin", "get_texture_origin");
	ADD_PROPERTY(PropertyInfo(Variant::COLOR, "modulate"), "set_modulate", "get_modulate");
	ADD_PROPERTY(PropertyInfo(Variant::OBJECT, "material", PROPERTY_HINT_RESOURCE_TYPE, "CanvasItemMaterial,ShaderMaterial"), "set_material", "get_material");
	ADD_PROPERTY(PropertyInfo(Variant::INT, "z_index"), "set_z_index", "get_z_index");
	ADD_PROPERTY(PropertyInfo(Variant::INT, "y_sort_origin"), "set_y_sort_origin", "get_y_sort_origin");
	ADD_GROUP("Terrains", "");
	ADD_PROPERTY(PropertyInfo(Variant::INT, "terrain_set"), "set_terrain_set", "get_terrain_set");
	ADD_PROPERTY(PropertyInfo(Variant::INT, "terrain"), "set_terrain", "get_terrain");
	ADD_GROUP("Miscellaneous", "");
	ADD_PROPERTY(PropertyInfo(Variant::FLOAT, "probability"), "set_probability", "get_probability");
	ADD_SIGNAL(MethodInfo("changed"));
}