### 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)

bool node_visible = tile_map_node->is_visible_in_tree();
	for (KeyValue<Vector2i, TileMapQuadrant> &E_quadrant : quadrant_map) {
		TileMapQuadrant &q = E_quadrant.value;
		for (const KeyValue<Vector2i, RID> &kv : q.occluders) {
			Transform2D xform;
			xform.set_origin(tile_map_node->map_to_local(kv.key));
			RS::get_singleton()->canvas_light_occluder_attach_to_canvas(kv.value, tile_map_node->get_canvas());
			RS::get_singleton()->canvas_light_occluder_set_transform(kv.value, tile_map_node->get_global_transform() * xform);
			RS::get_singleton()->canvas_light_occluder_set_enabled(kv.value, node_visible);
		}
	}
}
void TileMapLayer::notify_visibility_changed() {
	bool node_visible = tile_map_node->is_visible_in_tree();
	for (KeyValue<Vector2i, TileMapQuadrant> &E_quadrant : quadrant_map) {
		TileMapQuadrant &q = E_quadrant.value;
		
		for (const KeyValue<Vector2, Vector2i> &E_cell : q.local_to_map) {
			Transform2D xform;
			xform.set_origin(E_cell.key);
			for (const KeyValue<Vector2i, RID> &kv : q.occluders) {
				RS::get_singleton()->canvas_light_occluder_set_enabled(kv.value, node_visible);
			}
		}
	}
}
void TileMapLayer::notify_xform_changed() {