I think what's happening here is that, ordinarily:

# docker run --rm -ti centos bash
# yum -y install /usr/sbin/getenforce
# getenforce
Disabled

However, inside a SPC, we mount /host, which ends up pulling in /host/sys/fs/selinux into the visible namespace,

# atomic run centos/tools
# getenforce
Enforcing

And looking at strace I can see this:

statfs("/sys/fs/selinux", {f_type="SYSFS_MAGIC", f_bsize=4096, f_blocks=0, f_bfree=0, f_bavail=0, f_files=0, f_ffree=0, f_fsid={0, 0}, f_namelen=255, f_frsize=4096}) = 0
statfs("/selinux", 0x7ffc189c8d70)      = -1 ENOENT (No such file or directory)
brk(0)                                  = 0x198a000
brk(0x19ab000)                          = 0x19ab000
open("/proc/filesystems", O_RDONLY)     = 3
fstat(3, {st_mode=S_IFREG|0444, st_size=0, ...}) = 0
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f74d3979000
read(3, "nodev\tsysfs\nnodev\trootfs\nnodev\tb"..., 1024) = 392
stat("/etc/sysconfig/64bit_strstr_via_64bit_strstr_sse2_unaligned", 0x7ffc189c8c50) = -1 ENOENT (No such file or directory)
close(3)                                = 0
munmap(0x7f74d3979000, 4096)            = 0
open("/proc/mounts", O_RDONLY)          = 3
fstat(3, {st_mode=S_IFREG|0444, st_size=0, ...}) = 0
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f74d3979000
read(3, "rootfs / rootfs rw 0 0\n/dev/mapp"..., 1024) = 1024
read(3, "group/cpuacct,cpu cgroup rw,nosu"..., 1024) = 1024
read(3, "ae83bedbab09933f6832b7000372 /ho"..., 1024) = 1024
read(3, "host/var/lib/docker/devicemapper"..., 1024) = 1024
read(3, "er/mnt/43471a878cf339022b82f9e53"..., 1024) = 1024
read(3, "2b7000372/rootfs/sys/fs/cgroup/b"..., 1024) = 1024
read(3, "latime,attr2,inode64,noquota 0 0"..., 1024) = 1024
read(3, "atime,xattr,release_agent=/usr/l"..., 1024) = 1024
read(3, "inuxfs rw,relatime 0 0\ndebugfs /"..., 1024) = 1024
statfs("/host/sys/fs/selinux", {f_type=0xf97cff8c, f_bsize=4096, f_blocks=0, f_bfree=0, f_bavail=0, f_files=0, f_ffree=0, f_fsid={0, 0}, f_namelen=255, f_frsize=4096}) = 0
statfs("/host/sys/fs/selinux", {f_type=0xf97cff8c, f_bsize=4096, f_blocks=0, f_bfree=0, f_bavail=0, f_files=0, f_ffree=0, f_fsid={0, 0}, f_namelen=255, f_frsize=4096}) = 0
stat("/host/sys/fs/selinux", {st_mode=S_IFDIR|0755, st_size=0, ...}) = 0
close(3)                                = 0

You can see how libselinux worked out to look at /host/sys/fs/selinux presumably because it's looking for a selinuxfs mount anywhere it can find in /proc/mounts.

We can fix the issue, but this could be a potential problem. In that we don't want labeling and load_policy to work within a container.  For example if you are running a rhel6 system and you update selinux-policy package we don't want this to update the policy on the host, even though this is an SPC.

# docker run -it --rm --name tools1 -v /sys/fs/selinux:/sys/fs/selinux:ro  --privileged --ipc=host --net=host --pid=host -e HOST=/host -e NAME=tools -e IMAGE=centos/tools -v /run:/run -v /var/log:/var/log -v /etc/localtime:/etc/localtime -v /:/host centos/tools
# getenforce 
Disabled

So mounting in /sys/fs/selinux as ro fixes the problem.  I will add this to --spc

https://github.com/projectatomic/atomic/pull/455

Fixed in atomic-1.11.

Dan, moving this to atomic as per Comment 5.

the  -v /sys/fs/selinux:/sys/fs/selinux:ro has been added into atomic-1.12.2-2.el7.x86_64, and I can successfully run centos/tools image, so moving the bug to VERIFIED status.

[root@hp-dl360g9-04 /]# atomic run centos/tools
Using default tag: latest
Trying to pull repository docker.io/centos/tools ... 
latest: Pulling from docker.io/centos/tools
3d8673bd162a: Pull complete 
fe5ec1faff9a: Pull complete 
355a87ce8b4b: Pull complete 
038c4c85b886: Pull complete 
Digest: sha256:969858ac9feb2dbef50f0c8a12306aa1512ef7b23c98e11aecbb02f3191784c5
Status: Downloaded newer image for docker.io/centos/tools:latest
docker run -it --name tools --privileged --ipc=host --net=host --pid=host -e HOST=/host -e NAME=tools -e IMAGE=centos/tools -v /sys/fs/selinux:/sys/fs/selinux:ro -v /run:/run -v /var/log:/var/log -v /etc/localtime:/etc/localtime -v /:/host centos/tools

This container uses privileged security switches:

INFO: --ipc=host 
      Processes in this container can see and possibly interact with all semaphores and shared memory segments on the host as well as disables SELinux within the container.

INFO: --net=host 
      Processes in this container can listen to ports (and possibly rawip traffic) on the host's network.

INFO: --pid=host 
      Processes in this container can see and interact with all processes on the host and disables SELinux within the container.

INFO: --privileged 
      This container runs without separation and should be considered the same as root on your system.

For more information on these switches and their security implications, consult the manpage for 'docker run'.

[root@hp-dl360g9-04 /]# getenforce
Disabled

Since the problem described in this bug report should be
resolved in a recent advisory, it has been closed with a
resolution of ERRATA.

For information on the advisory, and where to find the updated
files, follow the link below.

If the solution does not work for you, open a new bug report.

https://rhn.redhat.com/errata/RHBA-2016-2628.html