As for the .htaccess it doesn't take preference over the server. I set the settings in ownCloud and it DOES take effect (shown in /var/www/client/web/owncloud/.htaccess) but still uses server preferences listed in
You mix up a few things here, the .htaccess works fine and overrides the settings in the global apache configuration on your server. A .htaccess file is a config file of the apache server and not a config file of the php binary, the php settings that you refer to like php_value or php_flag are settings for the apache module mod_php and not for the php-fcgi program. You can set values for php-fcgi in the php.ini field of the website, so its even easier then editing a .htaccess file manually, the syntax is the same that you find in the php.ini.