If I place that setting under the "custom top-level configuration" when I restart the nginx service I get the following error:
[emerg] 22847#0: "client_max_body_size" directive is duplicate in /etc/nginx/conf.d/websitename.conf

Because that setting already exists in proxy.conf it can only be overridden in a sub-config for example under the server {} section.

Yes that's on a per-website basis. I would like to be able to override it on a global basis so that it applies to all the web sites.

What resolved this issue for me was adding the following line to /etc/vsftpd.conf

seccomp_sandbox=NO

It seems that needs to be added to most 64-bit servers.

Yeah the difference is doing it from the nginx config doesn't work for this value. It only works properly if it's done from the PHP-FPM config. It might work for newer versions of nginx/fpm but not with the versions included in Debian 7 stable.

My original comment said "Right now I've tried adding the open_basedir config as a fastcgi_param under nginx but that does not work properly."

Hey Eugeny, it turns out you didn't actually do it properly. You added it to the sites nginx config.

For for eg. /etc/nginx/conf.d/website.conf contains the following line:
fastcgi_param PHP_VALUE open_basedir="/srv/mywebsite";

But what actually needs to happen is for the following line to be added to the site config in /etc/php5/fpm/php-fpm.conf
php_admin_value[open_basedir] = "/srv/mywebsite"
And it should allow it to be set to multiple paths for example this input should be allowed:
php_admin_value[open_basedir] = "/srv/mywebsite:/tmp:/usr/share/php5"