Sorry to see you being disappointed with this. This is how our internal management software is built and this cannot be overwritten. This was, actually, done this way for a reason few years ago and this would be the very first time I'm seeing someone being unhappy about this. What is the problem to have VPS hostname with a matching PTR record for your primary IP?
Having non-matching hostname and PTR would result in rejected email on mail servers where PTR checks are performed unless your mail server is configured to use some other value instead of the system hostname during SMTP session. There is absolutely nothing wrong with the PTR record set to server1.domain.com.