php.ini is read when the PHP module is loaded in both mod_php, FastCGI and FPM. In regular CGI mode, the config file have to be read at runtime because there’s no preforked processes of any kind.
I think the only real advantage of running PHP as a module inside the web server is that the configuration might be easier. You get a lot better performance when you run it in FastCGI or FPM mode and can use a threaded or evented (instead of forked) Apache, or when you can throw out Apache altogether.