The other issue of yours I could not reproduce. After installing all dependencies, including kernel-headers and kernel-devel, make and dkms both were able to locate header files and get the correct kernel version.
I just made a clean install, now of Fedora 24. After installing, I updated the system and added the dependencies:
dnf groupinstall "Development Tools" "Development Libraries"
dnf install kernel-headers kernel-devel dkms rpm-build
I still need to comment the line that sets the SKIPKERNEL flag to have a successful compile with dkms.
On Fedora 24 (x86_64) dkms version is 220.127.116.11-34.git.9e0394d.fc24 and make version is 4.1-5.fc24.
Do you remember doing something different with your install? Maybe I'm missing something on my system.