I doubt that safe_mode exploit will ever be fixed seeing as how PHP 6.0 will not have safe_mode. At least that's what was said back when 6.0 was in early development. openbase_dir although useful if someone does get around it in theory they should be unable to do any damage. PHP is running as their user they're going to need to find folders that have read and write for everyone to do any damage. So really not a ton they can do and considering suPHP which a lot of people use does not support openbase_dir and we're not reading about people suggesting mod_php is better.
Plus as I said if your server supports Perl then these c99, r57 ect. ect. shells are just a php entry point. If they can get a perl version up they do not have openbase_dir restrictions anyways and can run shell commands.