The biggest difference is that mod_perl isn't typically available on shared hosting so the choices are often mod_php or CGI/perl. So while the article correctly states both mod_perl and mod_php are good solutions vs. CGI, on a typical shared hosting service, you are using CGI with Perl so mod_php will be faster.

FastCGI is often available on shared hosting, however I'm guessing the vast majority of Perl scripts on shared hosting run under CGI and not FastCGI. Even something as simple as changing 'use CGI;' to 'use CGI::Fast;' won't often happen. It would be nice if there was a more transparent way to switch from using CGI.pm to CGI::Fast.

I didn't take the time to analyze the author's methodology, but he takes the time to explain what he did and provides the Perl and PHP code he used for the benchmarks. It should be straightforward for someone to try to reproduce his results.