I still think that btrfs with bees ( GitHub - Zygo/bees: Best-Effort Extent-Same, a btrfs dedupe agent ) is the direction one should look into if you really need dedupe on Qubes today.
btrfs on Qubes uses the file-reflink driver so the above will likely work.
I can’t speak to whether you might need to modify the dom0 kernel to complete the solution but if you do you might be able to get Qubes development team to take a PR.
B