How do i get a specific user metadata using custom metavalue outside of wordpress?

If you have billing_phone as user meta, which is the preferred way, that query would be incorrect. The advantage of utilizing custom user meta and adding a field for billing_phone would allow you to use get_users().

$user = get_users('meta_key' => 'billing_phone', 'meta_value' => $phone_number, 'fields' => 'ID');

The above would give you an array of User IDs that have the matching billing_phone meta value.