At work, we bundle all perl modules (including ones that we write) up into deb files for release to QA and to production. Makefiles that prompt for information make this process annoying.

On the other hand, automated build scripts are definitely less common than people installing modules using perl -MCPAN -e shell. I'd probably suggest that you make it as easy as possible for regular users to install in this way - which (IMHO) means prompting for information where needed.