### 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)

const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	if (!tile_set.is_valid()) {
		return HashMap<Vector2i, TileSet::TerrainsPattern>();
	}
	
	RBSet<TerrainConstraint> constraints = p_constraints;
	
	HashMap<Vector2i, TileSet::TerrainsPattern> output;
	
	for (int i = 0; i < p_to_replace.size(); i++) {
		const Vector2i &coords = p_to_replace[i];
		
		TileSet::TerrainsPattern current_pattern = TileSet::TerrainsPattern(*tile_set, p_terrain_set);
		TileMapCell cell = get_cell(coords);
		if (cell.source_id != TileSet::INVALID_SOURCE) {
			TileSetSource *source = *tile_set->get_source(cell.source_id);
			TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
			if (atlas_source) {