Rechunker removes some directories in /var, breaking some services

We build fedora-based images using bootc. After adding the rechunker we noticed some services breaking because of it removing directories in `/var` during the "Removing top level directory contents" step. One example: rechunker removes `/var/spool/at` resulting in `atd.service` breaking because it can't find this directory. Some other services noticed to be affected are `logrotate.service` and `plocate-updatedb.service` For some context, here's the `hhd-dev/rechunk` call in our workflow file: https://github.com/pocketblue/pocketblue/blob/8936423fbcb8113d68cf2be969a687e2d4714ce1/.github/workflows/helper-build-container.yml#L57