I'm running a private Zarafa server configured with apache 2.2 and php-fpm using mod_fastcgi instead of mod_php.
With php-fpm, you create php pools per app, that means that you configure your app with the right php flags in the /etc/php-fpm.d directory.
This also means that .htaccess files won't be able to deal with php_flag php_admin or php_value directives.

Just for the sanity of both .htaccess files for webaccess and webapp, i propose adding <IfModule mod_php5.c> directive, so when you use php-fpm you won't have to change those files:

Best regards,