Looks like you could point it at IPFS "MFS" mount (Mutable File System) instead of whatever directory it's using now for its normal local storage media store (which I assume exists?), and that'd do the trick. Files stored in IPFS (so mirrorable through that, or whatever it is that you've got in mind) but appearing as ordinary files with normal names, so the normal file storage media store might manage to Just Work.
[EDIT] Incidentally MFS is exactly what I wished existed back when was kinda halfway considering using IPFS for my personal files. Been added since the last time I looked in on the project. Was too easy to "lose" files in IPFS otherwise. That sort-of fixes the problem, at least, provided the file tree can also be replicated pretty easily.
It takes a little bit to work out why you want it and why its so much better in that unixy way many of us insist on vs git-lfs (supporting ipfs should be a clue there).
*as a warning some of the defaults in last years git-annex 7 versions were aggressively annexing files in the git archives but fixed now.
