My personal feeling is that it would be easier to achieve a reproducible setup with existing distributions if packaging practices were less messy. The current practice of running scripts as root when a package is installed, as well as messing with /etc, which should actually be reserved for configuration by the system owner/administrator (possibly using tools of course) is not good for reproducibility. OpenSolaris for instance now forbids postinstall scripts. Packages which really need to do things post-install must install a service or similar to handle that. I would love it if say Debian adjusted their policy to discourage installation scripts and files dropped into/changed in /etc at install time. I am sure this would be manageable on a medium term basis.