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What to do with a '.pm' that has to be customized?

[This is a diversion from 5.005 problems :-) ]

I maintain a Perl package, BioPerl, which has one '.pm' which is supposed to 
be customized for local characteristics, before installing. I'm wondering how 
to handle it and I would like to know if someone already got the problem:

1) Customize it for Debian and do not let users customize it. Unfortunately, 
the variables to define are really site-dependant.

2) Install it, but flag it as a conffile. May be lintian will not like 
conffiles in /usr/share/perl?

3) Rewrite the module to have it 'use' the real conffile, in /etc/bioperl... 
Difficult (especially if the upstream maintainer does not want to integrate my 
patches) but cleaner.

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