### 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_COND(!scenes.has(p_id));
	scenes.erase(p_id);
	scenes_ids.erase(p_id);
	emit_signal(SNAME("changed"));
}
int TileSetScenesCollectionSource::get_next_scene_tile_id() const {
	return next_scene_id;
}
bool TileSetScenesCollectionSource::_set(const StringName &p_name, const Variant &p_value) {
	Vector<String> components = String(p_name).split("/", true, 2);
	if (components.size() >= 2 && components[0] == "scenes" && components[1].is_valid_int()) {
		int scene_id = components[1].to_int();
		if (components.size() >= 3 && components[2] == "scene") {
			if (has_scene_tile_id(scene_id)) {
				set_scene_tile_scene(scene_id, p_value);
			} else {
				create_scene_tile(p_value, scene_id);
			}
			return true;
		} else if (components.size() >= 3 && components[2] == "display_placeholder") {
			if (!has_scene_tile_id(scene_id)) {
				create_scene_tile(p_value, scene_id);
			}
			return true;
		}
	}
	return false;
}
bool TileSetScenesCollectionSource::_get(const StringName &p_name, Variant &r_ret) const {