### 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)

int quad_size = get_effective_quadrant_size();
	
	return Vector2i(
			p_coords.x > 0 ? p_coords.x / quad_size : (p_coords.x - (quad_size - 1)) / quad_size,
			p_coords.y > 0 ? p_coords.y / quad_size : (p_coords.y - (quad_size - 1)) / quad_size);
}
HashMap<Vector2i, TileMapQuadrant>::Iterator TileMapLayer::_create_quadrant(const Vector2i &p_qk) {
	TileMapQuadrant q;
	q.coords = p_qk;
	rect_cache_dirty = true;
	
	RenderingServer *rs = RenderingServer::get_singleton();
	q.debug_canvas_item = rs->canvas_item_create();
	rs->canvas_item_set_z_index(q.debug_canvas_item, RS::CANVAS_ITEM_Z_MAX - 1);
	rs->canvas_item_set_parent(q.debug_canvas_item, tile_map_node->get_canvas_item());
	
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	if (tile_set.is_valid()) {
		_rendering_create_quadrant(&q);
	}
	return quadrant_map.insert(p_qk, q);
}
void TileMapLayer::_make_quadrant_dirty(HashMap<Vector2i, TileMapQuadrant>::Iterator Q) {