Separate apps is more common on Fly, yes.
What does your nginx do? You may not need it if all you need is load balancing. We already do that (as well as TLS termination).
If you do need to use nginx, you could use our private networking to reach each node.js instances. You’d probably have to somehow create a dynamic configuration.
For example, you can query all private IPs for an app by looking up AAAA records for your-app-name.internal. Unfortunately you can’t use that directly as an upstream in nginx because it will probably just use 1 of the instances returned by the DNS query.