I don’t think what you are seeing is unexpected: qa-bot-gh has two VMs running as it is a 2-process Fly app (process1 running in vm1 is named app, process2 running in vm2 is named worker).
You may want to rename the process named app to server or some such (why?).
As to where to find your migrated app’s fly.toml, I am not so sure, but someone else may be able to help you figure out.