It's true that system repos doesn't include everything, but you can create your own repositories if you really need to for a few things. In practice Fedora/EPEL are basically sufficient for my needs. Right now I'm deploying something with yocto, which is a bit more limited in slection, but it's pretty easy to add my own packages and it at least has hashes so things don't get replaced without me noticing (to be fair, I don't know if the security practices of open-embedded recipes are as strong as Fedora...).