Agreed. Specifically allowing non-standard locations to remain in packages would cause the FHS would be broken, this would mean:

- config files would be shoved all over the place, without being able to back up /etc as a config location or map frequently read data to var

- You couldn't partition your disks reaosnably beyond a single filesystem as there's no way to predict where apps will shove their junk

- Uninstalling apps would leave junk cron jobs and other files made manually rather than put into include dirs

- Your PATH would be exceedingly long

- You'd end up using 'find' a lot more to know where a particular library is.