I have this exact same problem on FC29. All you've said is true regarding the build
and install of the kernel modules for the rpmfusion-free-updates repo. The modules get
rebuilt by akmod just fine.
dnf provides /usr/lib/modules-load.d/VirtualBox.conf
VirtualBox-server-5.2.22-1.fc29.x86_64 : core part (host server) for VirtualBox
Repo : rpmfusion-free-updates
Filename : /usr/lib/modules-load.d/VirtualBox.conf
The only problem is that dracut doesn't seem to be run after the modules are built. I
always get the error during boot until I do a "dracut -f".
My best guess on this is that for some reason dracut is only done for the first akmod
build. I have
ls -1 /usr/src/akmods/*.latest
and the error I get is always related to vboxdrv and friends not being there.