alias sys="rpm-ostree"

Aliases are fine, just place them in your .bashrc and make sure they aren't going to conflict with any packages you have installed/will install. The only potential downside is if you install a package that adds an executable to your path with the same name as an alias, but you can just change the alias if that's the case. Since dnf/yum aren't installed in the atomic versions, you could even make an alias with one of those (and if you're in a toolbox, just use the one you don't have an alias for when installing packages). That guarantees you won't have a conflicting executable name from newly installed packages, and I'd say it makes a bit more sense than sys, but as long as you can remember it, it shouldn't realistically matter; just a suggestion.