Also file conflicts. Installing an RPM/ALPM/APK should warn you before it clobbers existing files. But for a one-off install script, all it takes is a missing environment variable or an extra space (`mv /etc/$INSTAALCONF /tmp`, `chown -R root /$MY_DATA_PATFH`), and suddenly you can't log on.

Of course unpredictability itself is also a security problem. I'm not even supposed to run partial updates that at least come from the same repository. I ain't gonna shovel random shell scripts into the mix and hope for the best.

Uninstalling can be a problem.

Versioning OTOH is often more problematic with distro package managers that can't support multiple versions of the same package.

Also inability to do user install is a big problem with distro managers.