I was able to fix my server to check the REQUEST_URI for ikiwiki.cgi and to continue processing if it was not found, passing $ENV{SEVER_NAME} . $ENV{REQUEST_URI} as the first parameter to cgi_page_from_404. However, my perl is terrible and I just made it work rather than figuring out exactly what to do to get it to work on both lighttpd and apache.
I was able to fix my server to check the REQUEST_URI for ikiwiki.cgi and to continue processing if it was not found, passing $ENV{SEVER_NAME} . $ENV{REQUEST_URI} as the first parameter to cgi_page_from_404. However, my perl is terrible and I just made it work rather than figuring out exactly what to do to get it to work on both lighttpd and apache.