### 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)

ERR_FAIL_COND(!p_tile_set.is_valid());
	ERR_FAIL_COND(!p_tile_set->has_source(p_atlas_source_id));
	ERR_FAIL_COND(!p_tile_set->get_source(p_atlas_source_id)->has_tile(p_atlas_coords));
	ERR_FAIL_COND(!p_tile_set->get_source(p_atlas_source_id)->has_alternative_tile(p_atlas_coords, p_alternative_tile));
	TileSetSource *source = *p_tile_set->get_source(p_atlas_source_id);
	TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
	if (atlas_source) {
		
		if (p_frame >= 0) {
			ERR_FAIL_INDEX(p_frame, atlas_source->get_tile_animation_frames_count(p_atlas_coords));
		}
		
		Ref<Texture2D> tex = atlas_source->get_runtime_texture();
		if (!tex.is_valid()) {
			return;
		}
		
		Vector2i grid_size = atlas_source->get_atlas_grid_size();
		if (p_atlas_coords.x >= grid_size.x || p_atlas_coords.y >= grid_size.y) {
			return;
		}
		
		const TileData *tile_data = p_tile_data_override ? p_tile_data_override : atlas_source->get_tile_data(p_atlas_coords, p_alternative_tile);
		
		Color modulate = tile_data->get_modulate() * p_modulation;
		
		Vector2 tile_offset = tile_data->get_texture_origin();
		
		Rect2 dest_rect;