It makes little sense to use a hybrid Perl/PHP product these days. MT was suffering from being a Perl/CGI product and patched it up with PHP only to still be eaten by WordPress. Too little too late.
The PHP stuff is, AFAICT, another way to write MT plugins.
I hope the Melody project will better enable the use of CGI::Application or others for dynamic publishing instead of PHP There are already extensions for that, e.g. http://oss.iteman.jp/wiki/2/A_Perl_based_dynamic_publishing_...