### 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_COND_MSG(!tile_map_node->is_inside_tree(), "A TileMap navigation map can only be changed while inside the SceneTree.");
	navigation_map = p_map;
	uses_world_navigation_map = p_map == tile_map_node->get_world_2d()->get_navigation_map();
}
RID TileMapLayer::get_navigation_map() const {
	if (navigation_map.is_valid()) {
		return navigation_map;
	}
	return RID();
}
void TileMapLayer::force_update() {
	clear_internals();
	recreate_internals();
}
void TileMapLayer::fix_invalid_tiles() {
	Ref<TileSet> tileset = tile_map_node->get_tileset();
	ERR_FAIL_COND_MSG(tileset.is_null(), "Cannot call fix_invalid_tiles() on a TileMap without a valid TileSet.");
	RBSet<Vector2i> coords;
	for (const KeyValue<Vector2i, TileMapCell> &E : tile_map) {
		TileSetSource *source = *tileset->get_source(E.value.source_id);
		if (!source || !source->has_tile(E.value.get_atlas_coords()) || !source->has_alternative_tile(E.value.get_atlas_coords(), E.value.alternative_tile)) {
			coords.insert(E.key);
		}
	}
	for (const Vector2i &E : coords) {
		set_cell(E, TileSet::INVALID_SOURCE, TileSetSource::INVALID_ATLAS_COORDS, TileSetSource::INVALID_TILE_ALTERNATIVE);
	}
}
bool TileMapLayer::has_body_rid(RID p_physics_body) const {