### 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 (used_rect_cache_dirty) {
		bool first = true;
		used_rect_cache = Rect2i();
		if (tile_map.size() > 0) {
			if (first) {
				used_rect_cache = Rect2i(tile_map.begin()->key.x, tile_map.begin()->key.y, 0, 0);
				first = false;
			}
			for (const KeyValue<Vector2i, TileMapCell> &E : tile_map) {
				used_rect_cache.expand_to(Vector2i(E.key.x, E.key.y));
			}
		}
		if (!first) { 
			used_rect_cache.size += Vector2i(1, 1); 
		}
		used_rect_cache_dirty = false;
	}
	return used_rect_cache;
}
void TileMapLayer::set_name(String p_name) {