### 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)

continue;
				}
				TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
				if (atlas_source) {
					const TileData *tile_data;
					if (q.runtime_tile_data_cache.has(E_cell)) {
						tile_data = q.runtime_tile_data_cache[E_cell];
					} else {
						tile_data = atlas_source->get_tile_data(c.get_atlas_coords(), c.alternative_tile);
					}
					for (int tile_set_physics_layer = 0; tile_set_physics_layer < tile_set->get_physics_layers_count(); tile_set_physics_layer++) {
						Ref<PhysicsMaterial> physics_material = tile_set->get_physics_layer_physics_material(tile_set_physics_layer);
						uint32_t physics_layer = tile_set->get_physics_layer_collision_layer(tile_set_physics_layer);
						uint32_t physics_mask = tile_set->get_physics_layer_collision_mask(tile_set_physics_layer);
						
						RID body = ps->body_create();
						bodies_coords[body] = E_cell;
						ps->body_set_mode(body, tile_map_node->is_collision_animatable() ? PhysicsServer2D::BODY_MODE_KINEMATIC : PhysicsServer2D::BODY_MODE_STATIC);
						ps->body_set_space(body, space);
						Transform2D xform;
						xform.set_origin(tile_map_node->map_to_local(E_cell));
						xform = gl_transform * xform;
						ps->body_set_state(body, PhysicsServer2D::BODY_STATE_TRANSFORM, xform);
						ps->body_attach_object_instance_id(body, tile_map_node->get_instance_id());
						ps->body_set_collision_layer(body, physics_layer);
						ps->body_set_collision_mask(body, physics_mask);
						ps->body_set_pickable(body, false);
						ps->body_set_state(body, PhysicsServer2D::BODY_STATE_LINEAR_VELOCITY, tile_data->get_constant_linear_velocity(tile_set_physics_layer));
						ps->body_set_state(body, PhysicsServer2D::BODY_STATE_ANGULAR_VELOCITY, tile_data->get_constant_angular_velocity(tile_set_physics_layer));
						if (!physics_material.is_valid()) {