### 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)

TypedArray<Vector2i> a;
	a.resize(tile_map.size());
	int i = 0;
	for (const KeyValue<Vector2i, TileMapCell> &E : tile_map) {
		Vector2i p(E.key.x, E.key.y);
		a[i++] = p;
	}
	return a;
}
TypedArray<Vector2i> TileMapLayer::get_used_cells_by_id(int p_source_id, const Vector2i p_atlas_coords, int p_alternative_tile) const {
	
	TypedArray<Vector2i> a;
	for (const KeyValue<Vector2i, TileMapCell> &E : tile_map) {
		if ((p_source_id == TileSet::INVALID_SOURCE || p_source_id == E.value.source_id) &&
				(p_atlas_coords == TileSetSource::INVALID_ATLAS_COORDS || p_atlas_coords == E.value.get_atlas_coords()) &&
				(p_alternative_tile == TileSetSource::INVALID_TILE_ALTERNATIVE || p_alternative_tile == E.value.alternative_tile)) {
			a.push_back(E.key);
		}
	}
	return a;
}
Rect2i TileMapLayer::get_used_rect() const {