How to reproduce:
cat <<'EOF' >/etc/systemd/system/a.service
[Service]
RuntimeDirectory=rd
RuntimeDirectoryPreserve=yes
ExecStart=/bin/sh -x -c 'id; ls -l /run'
User=systemd-coredump
EOF
systemctl daemon-reload
systemctl start a
ls -l d /run/rd
# drwxr-xr-x 2 systemd-coredump systemd-coredump 40 Jul 17 20:49 /run/rd
sed -i 's/^\(User\)/#\1/' /etc/systemd/system/a.service
systemctl daemon-reload
systemctl start a
ls -ld /run/rd
# drwxr-xr-x 2 systemd-coredump systemd-coredump 40 Jul 17 20:49 /run/rd
# should be
# drwxr-xr-x 2 root root 40 Jul 17 20:49 /run/rd
Using User=root explicitly works well
echo 'User=root' >>/etc/systemd/system/a.service
systemctl daemon-reload
systemctl start a
ls -ld /run/rd
# drwxr-xr-x 2 root root 40 Jul 17 20:49 /run/rd