The Debian package I have been using actually does put the configs in /etc/bird which makes sense, as it's basically a normal Debian in the eyes of the package.
You can make a package though, where everything lives under /config, preferably /config/opt - right? Like I said: Not a good idea to have your routing-engine and -config wiped after a software update. You can, however, put a "normal" BIRD install package into /config/data/firstboot/install-packages and have a script in /config/scripts/firstboot.d which may restore the config file (or a symlink to /config/bird.conf, which also survives the big culling). In that case the package gets re-installed early during the first boot after a FW update (and the script called). If the BIRD distribution depends on other packages, those also need to go into /config/data/firstboot/install-packages. And of course you need to have scripts updating the packages in /config/data/firstboot/install-packages, when you update them ... -c