file-reflink backed by the ZFS filesystem is definitely much more uncommon. I’ve only ever heard of one person with that setup.
There are different ZFS knobs that might be worth tuning for the file-reflink driver (recordsize) vs. the zfs driver ( volblocksize) to deal with fragmentation, but I can’t tell you anything specific about that. Nor about typical performance.
AFAIK there isn’t any difference in features. file-reflink implements all features of the Qubes OS storage API, and so does zfs I assume.
Implementation wise, there’s some symmetry in that file-reflink is relatively simple and maybe a bit more battle tested from usage (in general, not backed by the ZFS filesystem!), but reflinking uses a complex and recent feature of the ZFS filesystem (the block reference table); whereas the zfs driver is somewhat more complex and recent, but sticks to tried-and-true features of the ZFS filesystem.