rpm-ostree currently does not support DKMS, and it’s unlikely that’ll be implemented anytime soon, if ever. It does support akmods, though, which is the preferred way to build Kernel modules on Fedora. You could ask if the packager can build that way to support the Fedora Atomic editions.
If you need these Kernel modules now, I think your only option would be to build manually from source, but that has the downside of requiring a manual step every time the Kernel is updated.