As the saying goes, "There's more than one way to cat a file". In this case, it's not absolutely clear what you mean by 'the same process running', so I'll explain both possible issues.
If what you mean is that you have the same process ID running if you first do a 'systemctl ngix start', and then do a 'service ngix start'. This would be because if a daemon is already running, a 'start' process will not shut it down and start a new one. In such a situation, the result should be a no-op. Do a stop before you do a subsequent start, or use a restart command instead.
If you did do a stop (or a reboot) between the two start commands, and you're seeing ngix running in both cases -- with the same parameters to the command, even though the process IDs are different, then the 'problem' is that in both cases, the ultimate goal is to get ngix running. The locations of content and configuration files don't change. The options you want to use don't change just because different programs start them. It's pretty much just a case of 'all roads lead to Rome'.
Finally, if you suspect that systemctl and service are links to the same file, then try.
cmp `which systemctl` `which service`
That will tell you if systemctl and service both contain exactly the same code (and/or are links to the same file).