Searching for a reason, why git-buildpackage (to be more specific: git-pbuilder) from debian repository doesn’t use my settings from ~/.pbuilderrc, I found that sudo by default changes environment to that belonging to root. I shared with this with author of script: http://www.eyrie.org/~eagle/journal/2012-01/006.html
If you have similar problem, check if in: /etc/sudoers your user have at least SETENV or ALL permission. After that invoke sudo, with -E parameter e.g.: sudo -E cowbuilder.