It's not quite that strict. In php.ini file (quoting from the manual):
safe_mode_exec_dir string
If PHP is used in safe mode, system() and the other functions
executing system programs refuse to start programs that
are not in this directory.
The whole point is to give you control over what is allowed. You are free to specifiy /bin as the safe_mode directory, though lots of the benefits of same mode may go away if you do that. A safer course would be to create a private directory and link just those executable that (1) you actually are using and (2) you have reviewed in regard to security aspects.