Hey, I've been torrenting on Linux through the ProtonVPN program without issues for the past months.
I don't know the specifics because I'm new to Linux, but I followed the official guide on how to set it up and everything just worked. Don't even need to change the port in qBit, I can upload anyway as long as I pick a P2P server in Proton, and very fast too (depending of what people want me to seed), uncapped upload speed often nears my max upload bandwidth.
Also binding qBit to the VPN is not a problem, just follow the official guide. Tested it now, and if I disconnect the VPN, qBit shows a red world in the network status and speeds go to zero, so it works.
It's true that the Linux client is not as fully-fledged as the Windows one, but it's not unusable.
I'm on PoP!_OS if it can be of any help. If you have questions that might help you with using Proton on Linux feel free to ask and I'll try my best!
You must have made a mistake somewhere, as once I close the Proton VPN client (actual "close", as in the app is not running anymore) my qBit does stop downloading (just tested), although the rest of the system still has access to the network (must have something to do with how apps are installed on Linux, I guess).
In my qBit settings > advanced > network interface I read "tun0", and that's what I think was suggested in the official setup guide on Proton. What do you have?