You can convert a VT_DATE object into a UNIX timestamp with variant_date_to_timestamp and then format it with date, this should work regardless of the date format in the control panel.
$format = "Y-m-d";
$object = $recordset->Fields->Item("System.DateModified")->Value;
$timestamp = variant_date_to_timestamp($object);
echo date($format, $timestamp) . "\n";