mod_php vs cgi vs fast-cgi
Solution 1:
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.
Solution 2:
This link may help: http://2bits.com/articles/apache-fcgid-acceptable-performance-and-better-resource-utilization.html
Conclusion
If pure speed is what you are after, then stay with mod_php.
However, for better resource usage and efficiency, consider moving to fcgid.
Solution 3:
php.ini is read when the module is loaded in the case of an Apache module. PHP CGI uses a php interpreter executable like any other shell script would do. Since there is no state involved at each invocation, the config file would have to be read every single time in case of CGI.