Backups should be stored in CIA format, not the multi-part method the eShop CDN uses.
Carts do not contain the same data structure as eShop content, and would never be compatible with the way FreeShop installs games. Even if OP were to add the ability to specify a custom server.
If (And that's a big IF) OP were to add the functionality to specify a custom CDN, instead of relying on Nintendo's, you would need to re-create the exact same directory structure, with all of the same files, for it to work. It would also never allow custom folder structures or CIA/3ds files.
When Nintendo ditches the eShop CDN for 3DS (And you're looking at 10+ years from now, I'm guessing) someone will probably look into that, but more than likely you'll just get a prettier CIA manager. There's zero reason to implement anything like that at this point in time.