I know it is quite old, I'll just answer in case someone else needs the answer. What I usually do, is that I have a shell script which creates the .pkg file for me. In that script I set all the file permissions and ownership before packaging. Here is an example:
NAME="PKGFILENAME"
IDENTIFIER="com.pkg.APPNAME"
VERSION="1.0.0"
INSTALL_LOCATION="PATH_TO_WHERE_THE_FILES_SHOULD_BE_COPIED_ON_USERS_MACHINE"
ROOT_LOCATION="PATH_TO_WHERE_FILES_ARE_ON_YOUR_MASCHINE"
# Remove any unwanted .DS_Store files.
find "$ROOT_LOCATION" -name '*.DS_Store' -type f -delete
# put any command for changing the ownership or permissions here
chmod -R +r "$ROOT_LOCATION"
# Build package.
/usr/bin/pkgbuild \
--root "$ROOT_LOCATION" \
--install-location "$INSTALL_LOCATION" \
--identifier "$IDENTIFIER" \
--version "$VERSION" \
"$NAME.pkg"
save this something in a file like create-my-package.sh and run this in command line.