Whether those pitfalls are a good or a bad thing probably depends on the requirements. For example, if one would like to support config reloading the second pitfall would actually be a good thing.

I guess the issue is more a matter of style than any technical reason. It might be best to choose whatever one feels comfortable with.

It may even depend on how you view the configuration: If the configuration feels like part of the program, require or use might be better because it's heaviliy associated with module loading. That way, the final 1; in the configuration won't feel awkward, too. If the configuration is more external, and Perl is mostly used for syntactic convenience, I'd prefer do.