Invalid command ‘FcgidMaxProcesses’

Check your include directive. It appears httpd is trying to run your certificate file as if it was a configuration file. So the "---begin RSA key" at the start of certificate file is getting handled like an (invalid) command. In your main httpd.conf file, I'm betting your include is something like this: Include conf.d/ssl.crt/* when it should be more like this: Include conf.d/ssl.crt/*.conf or Include conf.d/*.conf

Include is used to pull in all the additional configuration files for other httpd modules. One of which is ssl.conf. However, you don't want those keys to be treated like config files, else you get the error you're seeing.

Putting php_flag etc in .htaccess is only possible when you are using mod_php. With CGI/FCGI, Apache settings cannot be used to configure PHP since it is not running within Apache.

Using CGI, if you need a site with a custom php.ini, the exact details would depend on how exactly you're running the PHP (CGI, mod_fastcgi (with or without php-fpm), mod_fcgid). For basic CGI you will need to create an alternate Action for php files in that site that executes a wrapper script containing something like /usr/bin/php5-cgi -c /some/alternate/php.ini