### 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)

Transform2D xform;
				xform.set_origin(tile_map_node->map_to_local(bodies_coords[body]));
				xform = tilemap_xform * xform;
				PhysicsServer2D::get_singleton()->body_set_state(body, PhysicsServer2D::BODY_STATE_TRANSFORM, xform);
			}
		}
	}
}
void TileMapLayer::notify_local_xform_changed() {
	if (!tile_map_node->is_inside_tree()) {
		return;
	}
	bool in_editor = false;
#ifdef TOOLS_ENABLED
	in_editor = Engine::get_singleton()->is_editor_hint();
#endif
	if (!tile_map_node->is_collision_animatable() || in_editor) {
		Transform2D gl_transform = tile_map_node->get_global_transform();
		for (KeyValue<Vector2i, TileMapQuadrant> &E : quadrant_map) {
			TileMapQuadrant &q = E.value;
			for (RID body : q.bodies) {
				Transform2D xform;
				xform.set_origin(tile_map_node->map_to_local(bodies_coords[body]));
				xform = gl_transform * xform;
				PhysicsServer2D::get_singleton()->body_set_state(body, PhysicsServer2D::BODY_STATE_TRANSFORM, xform);
			}
		}
	}
}
void TileMapLayer::notify_canvas_exited() {