I have customers with some insanely old stuff that still relies on a working cgi-bin setup where they can dump their (perl-based) scripts.

Before I just add some things manually (in the "Domains", "Own vhost Settings"), should I be looking at another method? I'm using Apache 2.4 (mpm_worker_module) and php-fpm. I see a "perl/CGI" section in the settings, but it looks like that's only available for nginx or lighttpd, correct?

no, it's not only for nginx or lighttpd - depending on your server, you might need to activate the Enable SuExec workaround but other than that, the customers needs to be allowed to execute perl (customer add/edit form) and he/she needs to add a directory option to allow a specific folder to execute perl-scripts (Extras- > Path options -> add one, specify path, check 'Execute perl/cgi')