Comment 2 for bug 623375

run_bootloader looks like this:

# Invoke bootloader
run_bootloader()
{
        # invoke policy conformant bootloader hooks
        if [ -d /etc/initramfs/post-update.d/ ]; then
                run-parts --arg=${version} --arg=${initramfs} \
                        /etc/initramfs/post-update.d/
                return 0
        fi

        # FIXME: to be removed postsqueeze release
[...]
        if flash-kernel --supported >/dev/null 2>&1; then
                flash-kernel ${version}
                return 0
        fi
}

Thus, I think that if you simply have flash-kernel create a /etc/initramfs/post-update.d/flash-kernel script (this could be done in Debian - see http://lists.debian.org/debian-kernel/2010/07/msg00078.html for the policy draft), then you could have that script honour some environment variable and that would be all you need.