### 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("get_terrains_count", "terrain_set"), &TileSet::get_terrains_count);
	ClassDB::bind_method(D_METHOD("add_terrain", "terrain_set", "to_position"), &TileSet::add_terrain, DEFVAL(-1));
	ClassDB::bind_method(D_METHOD("move_terrain", "terrain_set", "terrain_index", "to_position"), &TileSet::move_terrain);
	ClassDB::bind_method(D_METHOD("remove_terrain", "terrain_set", "terrain_index"), &TileSet::remove_terrain);
	ClassDB::bind_method(D_METHOD("set_terrain_name", "terrain_set", "terrain_index", "name"), &TileSet::set_terrain_name);
	ClassDB::bind_method(D_METHOD("get_terrain_name", "terrain_set", "terrain_index"), &TileSet::get_terrain_name);
	ClassDB::bind_method(D_METHOD("set_terrain_color", "terrain_set", "terrain_index", "color"), &TileSet::set_terrain_color);
	ClassDB::bind_method(D_METHOD("get_terrain_color", "terrain_set", "terrain_index"), &TileSet::get_terrain_color);
	
	ClassDB::bind_method(D_METHOD("get_navigation_layers_count"), &TileSet::get_navigation_layers_count);
	ClassDB::bind_method(D_METHOD("add_navigation_layer", "to_position"), &TileSet::add_navigation_layer, DEFVAL(-1));
	ClassDB::bind_method(D_METHOD("move_navigation_layer", "layer_index", "to_position"), &TileSet::move_navigation_layer);
	ClassDB::bind_method(D_METHOD("remove_navigation_layer", "layer_index"), &TileSet::remove_navigation_layer);
	ClassDB::bind_method(D_METHOD("set_navigation_layer_layers", "layer_index", "layers"), &TileSet::set_navigation_layer_layers);
	ClassDB::bind_method(D_METHOD("get_navigation_layer_layers", "layer_index"), &TileSet::get_navigation_layer_layers);
	ClassDB::bind_method(D_METHOD("set_navigation_layer_layer_value", "layer_index", "layer_number", "value"), &TileSet::set_navigation_layer_layer_value);
	ClassDB::bind_method(D_METHOD("get_navigation_layer_layer_value", "layer_index", "layer_number"), &TileSet::get_navigation_layer_layer_value);
	
	ClassDB::bind_method(D_METHOD("get_custom_data_layers_count"), &TileSet::get_custom_data_layers_count);
	ClassDB::bind_method(D_METHOD("add_custom_data_layer", "to_position"), &TileSet::add_custom_data_layer, DEFVAL(-1));
	ClassDB::bind_method(D_METHOD("move_custom_data_layer", "layer_index", "to_position"), &TileSet::move_custom_data_layer);
	ClassDB::bind_method(D_METHOD("remove_custom_data_layer", "layer_index"), &TileSet::remove_custom_data_layer);
	ClassDB::bind_method(D_METHOD("get_custom_data_layer_by_name", "layer_name"), &TileSet::get_custom_data_layer_by_name);
	ClassDB::bind_method(D_METHOD("set_custom_data_layer_name", "layer_index", "layer_name"), &TileSet::set_custom_data_layer_name);
	ClassDB::bind_method(D_METHOD("get_custom_data_layer_name", "layer_index"), &TileSet::get_custom_data_layer_name);
	ClassDB::bind_method(D_METHOD("set_custom_data_layer_type", "layer_index", "layer_type"), &TileSet::set_custom_data_layer_type);
	ClassDB::bind_method(D_METHOD("get_custom_data_layer_type", "layer_index"), &TileSet::get_custom_data_layer_type);
	
	ClassDB::bind_method(D_METHOD("set_source_level_tile_proxy", "source_from", "source_to"), &TileSet::set_source_level_tile_proxy);
	ClassDB::bind_method(D_METHOD("get_source_level_tile_proxy", "source_from"), &TileSet::get_source_level_tile_proxy);