### 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)

clear_instantiated_scenes();
	clear_internals();
	tile_map.clear();
	recreate_internals();
	used_rect_cache_dirty = true;
}
Ref<TileMapPattern> TileMapLayer::get_pattern(TypedArray<Vector2i> p_coords_array) {
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	ERR_FAIL_COND_V(!tile_set.is_valid(), nullptr);
	Ref<TileMapPattern> output;
	output.instantiate();
	if (p_coords_array.is_empty()) {
		return output;
	}
	Vector2i min = Vector2i(p_coords_array[0]);
	for (int i = 1; i < p_coords_array.size(); i++) {
		min = min.min(p_coords_array[i]);
	}
	Vector<Vector2i> coords_in_pattern_array;
	coords_in_pattern_array.resize(p_coords_array.size());
	Vector2i ensure_positive_offset;
	for (int i = 0; i < p_coords_array.size(); i++) {
		Vector2i coords = p_coords_array[i];
		Vector2i coords_in_pattern = coords - min;
		if (tile_set->get_tile_shape() != TileSet::TILE_SHAPE_SQUARE) {