I\'m using CloudFlare to hide original server IP address (preventing from attacks to the server, DDos...), but when I use PHPmailer on site for sending confirmation e-mails to t
Service PostmarkApp.com is good for this purpose. It is for transactional emails (not for marketing) and it's hiding IP address of the originating server.
You can't prevent that appearing because it's added by the receiving server, not the sending one, so it's out of your control.
Because you're relaying though, there's no particular reason that the origin server needs to be internet-accessible at all; the only external connection it needs is outbound SMTP to google's mail servers, so you can block everything else. If that firewalling is done upstream from your server, then it will be nicely insulated and not actually suffer any of the DDoS traffic.
This is more of a security or server fault question.