VPN Service configuration parameter "target" receive only a single IP value for a single IBM i server. We did that for a simple reason, stability. Let's say a company has a plethora of IBM i servers, running all through a single process is a single point of failure which in networking scenarios is actually a bad choice.
Having more than one VPN instance, each for one server is a better solution as if one of the services crash, only connections to that specific target will be broken. Other services will continue running.
Second reason is separation of users / server. This is possible with different passwords or TLS certificates. In other to use different configs, we need to run different instances.
However, as VPN service is made as easy as possible to use, reading config file and certificates are done from the same directory where VPN Service is running.
So, a simple solution is just to create multiple directories where each one contains VPN Service, config file and TLS certificates if used.
Please don't forget to use different listening ports and open redirections on your router / firewall for each of them.
That's all what is needed.