I know this is an old thread, but I ran into an issue under mod_perl where cgiapp_init was being called on every request, not just at server (or process) start. I did some searches and found this: http://old.nabble.com/cgi%3A%3Aapplication%3A%3Adispatch-and-modperl-td29916199.html
Summary: they're both called on every request. Not sure if it's a change since this thread was posted but the information here doesn't seem to be correct.
in reply to Re: In CGI::Application cgiapp_prerun vs. cgiapp_init?
in thread In CGI::Application cgiapp_prerun vs. cgiapp_init?