diverging clones of the same Qubes template
Precisely.
I have the base Fedora X template that Qubes ships, and a full clone of the template which is my main and only template, because I don’t need more. I could at any point in time erase the template theat Qubes OS ships, and I would reclaim what, 5 GB? My actually-used template is so far updated that pretty much nothing is in common with the base Fedora X template, so dedup would gain me exactly zero bytes, and waste some RAM for no good reason.
Currently, dedup is probably not worth using — in particular with a proper ZFS pool driver — except in niche cases. I could see how dedup would be useful after Qubes 4.1 when the file driver is deleted and the only thing remaining is the file-reflink driver (which under Qubes would make full copies of VM images, which then would benefit from dedup), but using the file-reflink driver with ZFS will be unbearable simply because it would take forever just to start a VM (ZFS master does not support reflink copies right now, and support for reflink is currently under a lengthy review process).