### 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(NavigationServer2D::get_singleton());
	if (!navigation_map.is_valid()) {
		if (layer_index_in_tile_map_node == 0 && tile_map_node->is_inside_tree()) {
			
			navigation_map = tile_map_node->get_world_2d()->get_navigation_map();
			uses_world_navigation_map = true;
		} else {
			RID new_layer_map = NavigationServer2D::get_singleton()->map_create();
			
			NavigationServer2D::get_singleton()->map_set_cell_size(new_layer_map, 1.0);
			NavigationServer2D::get_singleton()->map_set_active(new_layer_map, true);
			navigation_map = new_layer_map;
			uses_world_navigation_map = false;
		}
	}
}
void TileMapLayer::_navigation_cleanup() {