### 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)

HashMap<Vector2i, TileMapCell>::ConstIterator E = tile_map.find(p_coords);
	if (!E) {
		return TileSetSource::INVALID_TILE_ALTERNATIVE;
	}
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	if (p_use_proxies && tile_set.is_valid()) {
		Array proxyed = tile_set->map_tile_proxy(E->value.source_id, E->value.get_atlas_coords(), E->value.alternative_tile);
		return proxyed[2];
	}
	return E->value.alternative_tile;
}
TileData *TileMapLayer::get_cell_tile_data(const Vector2i &p_coords, bool p_use_proxies) const {
	int source_id = get_cell_source_id(p_coords, p_use_proxies);
	if (source_id == TileSet::INVALID_SOURCE) {
		return nullptr;
	}
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	Ref<TileSetAtlasSource> source = tile_set->get_source(source_id);
	if (source.is_valid()) {
		return source->get_tile_data(get_cell_atlas_coords(p_coords, p_use_proxies), get_cell_alternative_tile(p_coords, p_use_proxies));
	}
	return nullptr;
}
void TileMapLayer::clear() {