### 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 (instantiated_scenes.is_empty()) {
		for (const KeyValue<Vector2i, String> &E : p_quadrant->scenes) {
			Node *node = tile_map_node->get_node_or_null(E.value);
			if (node) {
				node->queue_free();
			}
		}
		p_quadrant->scenes.clear();
	}
}
void TileMapLayer::_scenes_draw_quadrant_debug(TileMapQuadrant *p_quadrant) {
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	ERR_FAIL_COND(!tile_set.is_valid());
	if (!Engine::get_singleton()->is_editor_hint()) {
		return;
	}
	
	RenderingServer *rs = RenderingServer::get_singleton();
	Vector2 quadrant_pos = tile_map_node->map_to_local(p_quadrant->coords * get_effective_quadrant_size());
	for (const Vector2i &E_cell : p_quadrant->cells) {
		const TileMapCell &c = get_cell(E_cell, true);
		TileSetSource *source;