The key difference was that you had to adapt your Perl to work with mod_perl, where mod_php "just worked" in the same way CGIs did -- you could throw your .php scripts up over FTP and they'd benefit from mod_php being installed. This was a massive difference in practice.
EDIT: I have managed to dig out slides from a talk I gave about this a million years ago with a good section that walks through history of how all this worked, CGIs, mod_perl, PSGI etc, for anyone who wants a brief history lesson: https://www.slideshare.net/slideshow/psgi-and-plack-from-fir...
EDIT: I have managed to dig out slides from a talk I gave about this a million years ago with a good section that walks through history of how all this worked, CGIs, mod_perl, PSGI etc, for anyone who wants a brief history lesson: https://www.slideshare.net/slideshow/psgi-and-plack-from-fir...