### 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)

ERR_FAIL_NULL(PhysicsServer2D::get_singleton());
	for (RID body : p_quadrant->bodies) {
		bodies_coords.erase(body);
		PhysicsServer2D::get_singleton()->free(body);
	}
	p_quadrant->bodies.clear();
}
void TileMapLayer::_physics_draw_quadrant_debug(TileMapQuadrant *p_quadrant) {
	
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	ERR_FAIL_COND(!tile_set.is_valid());
	if (!tile_map_node->get_tree()) {
		return;
	}
	bool show_collision = false;
	switch (tile_map_node->get_collision_visibility_mode()) {
		case TileMap::VISIBILITY_MODE_DEFAULT:
			show_collision = !Engine::get_singleton()->is_editor_hint() && tile_map_node->get_tree()->is_debugging_collisions_hint();
			break;
		case TileMap::VISIBILITY_MODE_FORCE_HIDE:
			show_collision = false;
			break;
		case TileMap::VISIBILITY_MODE_FORCE_SHOW:
			show_collision = true;
			break;