### 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, custom_data_layers.size(), "");
	return custom_data_layers[p_layer_id].name;
}
void TileSet::set_custom_data_layer_type(int p_layer_id, Variant::Type p_value) {
	ERR_FAIL_INDEX(p_layer_id, custom_data_layers.size());
	custom_data_layers.write[p_layer_id].type = p_value;
	for (KeyValue<int, Ref<TileSetSource>> &E_source : sources) {
		E_source.value->notify_tile_data_properties_should_change();
	}
	emit_changed();
}
Variant::Type TileSet::get_custom_data_layer_type(int p_layer_id) const {
	ERR_FAIL_INDEX_V(p_layer_id, custom_data_layers.size(), Variant::NIL);
	return custom_data_layers[p_layer_id].type;
}
void TileSet::set_source_level_tile_proxy(int p_source_from, int p_source_to) {
	ERR_FAIL_COND(p_source_from == TileSet::INVALID_SOURCE || p_source_to == TileSet::INVALID_SOURCE);
	source_level_proxies[p_source_from] = p_source_to;
	emit_changed();
}
int TileSet::get_source_level_tile_proxy(int p_source_from) {
	ERR_FAIL_COND_V(!source_level_proxies.has(p_source_from), TileSet::INVALID_SOURCE);
	return source_level_proxies[p_source_from];
}
bool TileSet::has_source_level_tile_proxy(int p_source_from) {
	return source_level_proxies.has(p_source_from);
}
void TileSet::remove_source_level_tile_proxy(int p_source_from) {