I don’t have a great answer for you, but hopefully I can provide some ideas that I hope can get your ideas flowing
Use a config file and use the built-in VPN configuration. Not very flexible, but you can be pretty confident it should work.
Use some containers (with docker or podman) to set up a qbit and a gluetun container.
Use the new version of the app for linux if you’re not already.
Whatever you do, I hope you look into the option in advanced settings in qbit to a specific network interface so it only works through the VPN. Unfortunately you definitely right that the Linux app is a second class citizen :/