This suggestion (provide both a system-wide and user-specific config) is very sensible and helps alleviate the central problem, but I don't think it eliminates it. What should the installer do when confronted with an existing system-wide configuration file? Overwriting it is harmless only
if all customization has been confined to the user-specific files. Most likely, you're stuck with doing something like silently creating a "config.new" file, and leaving "config" alone. For extra-credit, you could examine the existing config file to see if it differs from the default (compare MD5 hashes?) and overwrite if no customization has been done. And if you want to go above and beyond, you could try to merge your changes into the existing file.
Note: asking the user about this in the middle of an installation is to be avoided on penalty of death. Think about someone using CPANPLUS to install a module with a cascading series of dependencies involving dozens of modules. What if every other package wanted to politely ask a question about something?
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