### 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)

if (p_layer >= 0) {
		TILEMAP_CALL_FOR_LAYER(p_layer, force_update);
	} else {
		_clear_internals();
		_recreate_internals();
	}
}
#ifdef TOOLS_ENABLED
Rect2 TileMap::_edit_get_rect() const {
	
	if (layers.is_empty()) {
		return Rect2();
	}
	bool any_changed = false;
	bool changed = false;
	Rect2 rect = layers[0]->get_rect(changed);
	any_changed |= changed;
	for (unsigned int i = 1; i < layers.size(); i++) {
		rect = rect.merge(layers[i]->get_rect(changed));
		any_changed |= changed;
	}
	const_cast<TileMap *>(this)->item_rect_changed(any_changed);
	return rect;
}
#endif
bool TileMap::_set(const StringName &p_name, const Variant &p_value) {