The server is using cPanel.
Further testing reveals that it does work but with some file extension oddities. I've been testing numerous different PHP configurations so some non-standard file extensions were being used to differentiate the versions.
When the script handler is set for .php53 it would not run with suexec (scripts ran as nobody). When I changed this to .php5 it did work. I've tried other random extensions as well and it seems like there is some kind of limit as to what extensions suexec will recognize. Is this correct?