So you're trying to get 2 instances of qbt behind the same Gluetun vpn container?
I don't use Qbt but I certainly have done in the past. Am I correct in remembering that in the gui you can change the port?
If so, maybe what you could do is set up your stack with 1 instance in, go into the GUI and change the port on the service to 8000 or 8081 or whatever.
Map that port in your Gluetun config and leave the default port open for QBT, and add a second instance to the stack with a different name and addresses for the config files.