### Godot version

4.2.dev3.official[013e8e3af]

### System information

Godot v4.2.dev3 - Arch Linux #1 SMP PREEMPT_DYNAMIC Fri, 11 Aug 2023 11:03:36 +0000 - X11 - GLES3 (Compatibility) - NVIDIA GeForce RTX 2060 (nvidia; 535.98) - Intel(R) Core(TM) i7-10875H CPU @ 2.30GHz (16 Threads)

### Issue description

`TileMap.get_used_cells_by_id()` seems not work as expected.
It seems that this method will return the same result as "TileMap.get_used_cells()" since Godot 4.2dev2.
The arguments  (`source_id: int`, `atlas_coords: Vector2i`, `alternative_tile: int`) of `get_used_cells_by_id()` seems not make the filter working as expected.  It would only return the same result as `get_used_cells()`, contains all the tiles on the layer.

### Steps to reproduce

1. create a tilemap scene
2. attach a tileset, that contains  at least 2 tiles , paint some tiles.
3. calls Tilemap.get_used_cells_by_id(layer, source_id, atlas_coords,alternative_tile)
4. run it

### Minimal reproduction project

run tile_map.tscn by Godot4dev3 (or custom build)
[tilemap_debug.zip](https://github.com/godotengine/godot/files/12369631/tilemap_debug.zip)

layers[index]->set_tile_data(format, p_value);
			emit_signal(CoreStringNames::get_singleton()->changed);
			return true;
		} else {
			return false;
		}
	}
	return false;
}
bool TileMap::_get(const StringName &p_name, Variant &r_ret) const {
	Vector<String> components = String(p_name).split("/", true, 2);
	if (p_name == "format") {
		r_ret = TileMapLayer::FORMAT_MAX - 1; 
		return true;
	} else if (components.size() == 2 && components[0].begins_with("layer_") && components[0].trim_prefix("layer_").is_valid_int()) {
		int index = components[0].trim_prefix("layer_").to_int();
		if (index < 0 || index >= (int)layers.size()) {
			return false;
		}
		if (components[1] == "name") {
			r_ret = get_layer_name(index);
			return true;
		} else if (components[1] == "enabled") {
			r_ret = is_layer_enabled(index);
			return true;
		} else if (components[1] == "modulate") {
			r_ret = get_layer_modulate(index);
			return true;
		} else if (components[1] == "y_sort_enabled") {
			r_ret = is_layer_y_sort_enabled(index);