Basically installing packages. You’re fine if you default to using
- flatpaks for gui apps
- brew for cli programs
- distrobox when building from source or when you need good control over the package environment (e.g. when installing a latex editor and only the latex packages you want)
- layer packages on host with “rpm-ostree install” when the program needs tight integration with the host (e.g. VPN software)
Also, you shouldn’t edit files in /usr, but I’ve never run into that limitation. You can still edit other top-level directorys like /etc .
That’s about it.
As per my other comment:
Do your latex work inside a distrobox and you’re fine.
I’m not sure if you can layer another window manager on top. You may have to create a custom image for that