### 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)

prev_material = mat;
						prev_z_index = tile_z_index;
					} else {
						
						ci = prev_ci;
					}
					
					real_t random_animation_offset = 0.0;
					if (atlas_source->get_tile_animation_mode(c.get_atlas_coords()) != TileSetAtlasSource::TILE_ANIMATION_MODE_DEFAULT) {
						Array to_hash;
						to_hash.push_back(E_cell.key);
						to_hash.push_back(get_instance_id()); 
						random_animation_offset = RandomPCG(to_hash.hash()).randf();
					}
					
					tile_map_node->draw_tile(ci, E_cell.key - tile_position, tile_set, c.source_id, c.get_atlas_coords(), c.alternative_tile, -1, tile_map_node->get_self_modulate(), tile_data, random_animation_offset);
					
					for (int i = 0; i < tile_set->get_occlusion_layers_count(); i++) {
						Transform2D xform;
						xform.set_origin(E_cell.key);
						if (tile_data->get_occluder(i).is_valid()) {
							RID occluder_id = rs->canvas_light_occluder_create();
							rs->canvas_light_occluder_set_enabled(occluder_id, node_visible);
							rs->canvas_light_occluder_set_transform(occluder_id, tile_map_node->get_global_transform() * xform);
							rs->canvas_light_occluder_set_polygon(occluder_id, tile_data->get_occluder(i)->get_rid());
							rs->canvas_light_occluder_attach_to_canvas(occluder_id, tile_map_node->get_canvas());
							rs->canvas_light_occluder_set_light_mask(occluder_id, tile_set->get_occlusion_layer_light_mask(i));
							q.occluders[E_cell.value] = occluder_id;
						}
					}