The .service, zoneinfo, /opt, /rkt files were obviously not copied from the host but created or modified at run-time. They just appear here because I use the command find so it prints everything...
Tested on Debian-Sid with systemd-v220. Of course, it's going to be a different list on a different distribution...
# pwd
/var/lib/rkt/pods/run/04ffd940-4597-4931-bae2-2d2a93a71d4c/overlay/sha512-8c2140d625b5f176ed176963e63acb1d99b9096cc37d88e3683bd083cfc2ba53/upper
# find
.
./usr
./usr/bin
./usr/bin/bash
./usr/bin/systemctl
./usr/lib
./usr/lib/systemd
./usr/lib/systemd/system
./usr/lib/systemd/system/default.target.wants
./usr/lib/systemd/system/default.target.wants/sha512-e17fc826c76437429a085f2c276d3feb.service
./usr/lib/systemd/system/sha512-e17fc826c76437429a085f2c276d3feb.service
./usr/lib/systemd/system/[email protected]
./usr/lib/systemd/systemd
./usr/share
./usr/share/zoneinfo
./usr/share/zoneinfo/Europe
./usr/share/zoneinfo/Europe/Berlin
./opt
./opt/stage2
./opt/stage2/sha512-e17fc826c76437429a085f2c276d3feb
./opt/stage2/sha512-e17fc826c76437429a085f2c276d3feb/rootfs
./opt/stage2/sha512-e17fc826c76437429a085f2c276d3feb/manifest
./lib
./lib/systemd
./lib/systemd/systemd-shutdown
./lib/x86_64-linux-gnu
./lib/x86_64-linux-gnu/libpcre.so.3
./lib/x86_64-linux-gnu/libnss_mdns_minimal.so.2
./lib/x86_64-linux-gnu/libcap.so.2.24
./lib/x86_64-linux-gnu/libgcrypt.so.20.0.3
./lib/x86_64-linux-gnu/libaudit.so.1
./lib/x86_64-linux-gnu/liblzma.so.5.0.0
./lib/x86_64-linux-gnu/libmount.so.1
./lib/x86_64-linux-gnu/libtinfo.so.5
./lib/x86_64-linux-gnu/libnsl.so.1
./lib/x86_64-linux-gnu/libpcre.so.3.13.1
./lib/x86_64-linux-gnu/libattr.so.1
./lib/x86_64-linux-gnu/libkmod.so.2
./lib/x86_64-linux-gnu/libncurses.so.5
./lib/x86_64-linux-gnu/libapparmor.so.1
./lib/x86_64-linux-gnu/libnss_dns.so.2
./lib/x86_64-linux-gnu/libnss_compat-2.19.so
./lib/x86_64-linux-gnu/libnsl-2.19.so
./lib/x86_64-linux-gnu/libnss_nisplus.so.2
./lib/x86_64-linux-gnu/libgcrypt.so.20
./lib/x86_64-linux-gnu/libgpg-error.so.0.13.0
./lib/x86_64-linux-gnu/libapparmor.so.1.2.1
./lib/x86_64-linux-gnu/libnss_compat.so.2
./lib/x86_64-linux-gnu/libpthread-2.19.so
./lib/x86_64-linux-gnu/libdl.so.2
./lib/x86_64-linux-gnu/liblzma.so.5
./lib/x86_64-linux-gnu/libnss_mdns6.so.2
./lib/x86_64-linux-gnu/libnss_mdns4.so.2
./lib/x86_64-linux-gnu/libc-2.19.so
./lib/x86_64-linux-gnu/libnss_dns-2.19.so
./lib/x86_64-linux-gnu/libnss_hesiod.so.2
./lib/x86_64-linux-gnu/libpam.so.0.83.1
./lib/x86_64-linux-gnu/libnss_mdns4_minimal.so.2
./lib/x86_64-linux-gnu/libnss_mdns.so.2
./lib/x86_64-linux-gnu/libpthread.so.0
./lib/x86_64-linux-gnu/libcap.so.2
./lib/x86_64-linux-gnu/libgpg-error.so.0
./lib/x86_64-linux-gnu/libblkid.so.1
./lib/x86_64-linux-gnu/libaudit.so.1.0.0
./lib/x86_64-linux-gnu/libkmod.so.2.2.8
./lib/x86_64-linux-gnu/libncurses.so.5.9
./lib/x86_64-linux-gnu/libpam.so.0
./lib/x86_64-linux-gnu/libdl-2.19.so
./lib/x86_64-linux-gnu/libc.so.6
./lib/x86_64-linux-gnu/libblkid.so.1.1.0
./lib/x86_64-linux-gnu/libresolv.so.2
./lib/x86_64-linux-gnu/libnss_nis-2.19.so
./lib/x86_64-linux-gnu/libtinfo.so.5.9
./lib/x86_64-linux-gnu/libnss_mdns6_minimal.so.2
./lib/x86_64-linux-gnu/libresolv-2.19.so
./lib/x86_64-linux-gnu/libnss_files-2.19.so
./lib/x86_64-linux-gnu/libuuid.so.1
./lib/x86_64-linux-gnu/libnss_nis.so.2
./lib/x86_64-linux-gnu/librt.so.1
./lib/x86_64-linux-gnu/libuuid.so.1.3.0
./lib/x86_64-linux-gnu/libselinux.so.1
./lib/x86_64-linux-gnu/libnss_nisplus-2.19.so
./lib/x86_64-linux-gnu/libattr.so.1.1.0
./lib/x86_64-linux-gnu/ld-2.19.so
./lib/x86_64-linux-gnu/libnss_files.so.2
./lib/x86_64-linux-gnu/librt-2.19.so
./lib/x86_64-linux-gnu/libnss_hesiod-2.19.so
./lib/x86_64-linux-gnu/libmount.so.1.1.0
./lib/x86_64-linux-gnu/libnss_myhostname.so.2
./rkt
./rkt/env
./rkt/env/sha512-e17fc826c76437429a085f2c276d3feb
./rkt/status
./sys
./lib64
./lib64/ld-linux-x86-64.so.2