To expand upon that, I had something similar to the OP’s setup at one point, and I found things worked a lot better when the files could be moved on the same volume, rather than appearing as separate volumes (because they were mounted separately). I ended up re-engineering my whole setup for that and it’s much faster now.
As for duplicates… I assume this is so you can continue seeding after the file has been moved? I can’t think of anything that would fit the bill for that off the top of my head. Ideally, I think you’d want QBT to just start serving from the new location instead, though I admit hard links does sound like a solution that could work.
And after Googling, it seems like it already does hard links for torrents for this exact reason. I think if you just map /media (and drop the 2 maps you have after that) things will work like you want.
And incentivize them to raise it? No thanks!