The warning for the previous website literally means that, if a "http://domain.com/" web request arrives, NGINX won't know whether it should go to the first server{}, or to the second one.

that's because first one listens at www.example.com:80, and second one listens at example.com:80, therefore - no conflict

Only when, like this time, you setup another nginx server to handle port 80

Remove port 80 from the actual website, because you use the custom server entry to handle this port.

The warning appears because both your websites listen at http://domain.com:80

This looks perfectly correct and works on my system. What does nginx -t say?

Please post the full generated website config file.

That should work just fine in "Custom top level configuration"

That's exactly what "Custom top level configuration" box is for. If you need configuration in the same server block, just use the other configuration field.