### 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)

}
	HashMap<Vector2i, TileSet::TerrainsPattern> terrain_fill_output = terrain_fill_path(vector_path, p_terrain_set, p_terrain, p_ignore_empty_terrains);
	for (const KeyValue<Vector2i, TileSet::TerrainsPattern> &kv : terrain_fill_output) {
		if (painted_set.has(kv.key)) {
			
			TileMapCell c = tile_set->get_random_tile_from_terrains_pattern(p_terrain_set, kv.value);
			set_cell(kv.key, c.source_id, c.get_atlas_coords(), c.alternative_tile);
		} else {
			
			TileSet::TerrainsPattern in_map_terrain_pattern = TileSet::TerrainsPattern(*tile_set, p_terrain_set);
			TileMapCell cell = get_cell(kv.key);
			if (cell.source_id != TileSet::INVALID_SOURCE) {
				TileSetSource *source = *tile_set->get_source(cell.source_id);
				TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
				if (atlas_source) {
					
					TileData *tile_data = atlas_source->get_tile_data(cell.get_atlas_coords(), cell.alternative_tile);
					if (tile_data && tile_data->get_terrain_set() == p_terrain_set) {
						in_map_terrain_pattern = tile_data->get_terrains_pattern();
					}
				}
			}
			if (in_map_terrain_pattern != kv.value) {
				TileMapCell c = tile_set->get_random_tile_from_terrains_pattern(p_terrain_set, kv.value);
				set_cell(kv.key, c.source_id, c.get_atlas_coords(), c.alternative_tile);
			}
		}
	}
}
TypedArray<Vector2i> TileMapLayer::get_used_cells() const {