To get SDL_version.h on regular Fedora, you’d need to sudo dnf install sdl2-compat-devel and that should do it.
Unfortunately, Fedora Atomic is more like Android or iOS, where you can’t just install something into the system, you need to set up a special isolated development environment. I’m afraid that’s not something I’m familiar with. If nobody here has experience with development on Fedora Atomic, you might be able to get more help in a Fedora-specific community.