What causes permission to be denied for mounting rootfs, home, messeage queue, kernel file system, during boot?

My Fedora 27 x64 fails to boot after hard reset. It shows:

Failed to mount POSIX Message Queue File System,
Failed to start Remount and Kernel File Systems,
Failed to mount Kernel Debug File System,
Failed to mount Huge Pages File System [3]

and lots of other failures comes after these. See https://photos.app.goo.gl/qBUxT40zA2MTLTwO2

In all these cases

Failed at step EXEC spawning /usr/bin/mount: Permission denied

is given as a reason. How can it be? Doesn't it recognize it's own filesystems?

I have 3 kernels:

vmlinuz-4.14.16-300.fc27.x86_64
vmlinuz-4.15.13-300.fc27.x86_64
vmlinuz-4.15.14-300.fc27.x86_64

no matter which one I try to boot the same happens.

So far I have:

1. Checked filesystem integrity with fsck. All partitions are clean.
2. Checked disk health reported by SMART and performed both - short and long tests. Disk is perfectly healthy.
3. Rebuilt initramfs. Mounted boot, proc, sys, dev in /mnt, chroot and sudo dracut.

Followed suggestions and:

4. Performed fsck -f on /dev/mapper/fedora-home, got:

   tree extents for i-node 524820 (on level 2) could be narrower. Fix?<y>Y

Allowed to fix this.

And the same for /dev/mapper/fedora-root, /dev/sda1 (boot partition) confirmed they are clean. One more error of the same kind was found for an extra partition for data files.

5. rpm -V --all | grep -v " [cg] " returned as follows:

.M.......    /run/libgpod
..5....T.    /var/lib/selinux/targeted/active/commit_num
.......T.    /var/lib/selinux/targeted/active/file_contexts
.......T.    /var/lib/selinux/targeted/active/homedir_template
S.5....T.    /var/lib/selinux/targeted/active/policy.kern
.M.....T.    /var/lib/selinux/targeted/active/seusers
.M.....T.    /var/lib/selinux/targeted/active/users_extra
.M.......    /var/run/pluto
not exists   /var/run/abrt
.M.......    /var/log/audit
not exists   /usr/lib/systemd/system-preset/85-display-manager.preset
S.5....T.    /usr/share/icons/Crux/icon-theme.cache
S.5....T.    /usr/share/icons/Mist/icon-theme.cache

6. rpm -V "$(rpm -q --whatprovides /usr/bin/mount)"
   .M....G..  g /var/log/lastlog

7. fixfiles check /usr

   libsemanage.semanage_make_sandbox: Error removing old sandbox directory /var/lib/selinux/targeted/tmp. (Read only file system). 
   genhomedircon: Could not begin transaction: Read only file system

Among many lines similar to to the one below:

Would relabel /usr/src/handbrake/trunk/build/contrib/lib from unconfined_u:object_r:usr_t:s0 to unconfined_u:object_r:lib_t:s0

Would relabel /usr/sbin/mount.nilfs2 from unconfined_u:object_r:bin_t:s0 to unconfined_u:object_r:mount_exec_t:s0
Would relabel /usr/sbin/umount.nilfs2 from unconfined_u:object_r:bin_t:s0 to unconfined_u:object_r:mount_exec_t:s0
Would relabel /usr/sbin/mkfs.nilfs2 from unconfined_u:object_r:bin_t:s0 to unconfined_u:object_r:fsadm_exec_t:s0

8. Proved RAM works fine - memtest86 didn't find any errors during 3.5 passes and over 8h test time.

   9. Disabled SELinux (SELinux=disabled in /etc/selinux/config) and restarted. System started without any error! This proves problem is in SELinux policies. I believe I should start with checking those 6 top SELinux policies that have been changed somehow (see p. 5). The question is how to do it wisely.

9. Checked local modifications to SELinux config files and file_contexts:

   semanage module -C -l
   Module name              Priority  Language
   semanage fcontext -C -l
   fcontext SELinux                                 type               Context
   /usr/bin/mount                                     all files          system_u:object_r:samba_share_t:s0
   /usr/share/dnfdaemon/dnfdaemon-system              all files          system_u:object_r:rpm_exec_t:s0
   /var/run/media/przemek/extra(/.*)?                 all files          system_u:object_r:samba_share_t:s0
   /var/www/html/photo                                all files          system_u:object_r:httpd_sys_rw_content_t:s0
   /var/www/html/photo/_cache                         all files          system_u:object_r:httpd_sys_rw_content_t:s0
   /var/www/html/photo/config                         all files          system_u:object_r:httpd_sys_rw_content_t:s0
   /var/www/html/photo/content                        all files          system_u:object_r:httpd_sys_rw_content_t:s0
   /var/www/html/photo/content/folders.json           all files          system_u:object_r:httpd_sys_rw_content_t:s0
   /var/www/html/photo/iv-config/language             all files          system_u:object_r:httpd_sys_rw_content_t:s0

Interestingly fcontext of the /usr/bin/mount has changed.

The system runs 24h/day as a simple home server (www, mail, etc.). From time to time (say once a few weeks) it freezes completely. HDD keeps writing something (repetitive, although irregular sound). No reaction to keyboard, mouse, remote SSH access. Many times I have tried to leave it overnight, but it does not recover, so I am forced to hard reset it each time this happens. This time I haven't waited, but hard reset it after just a few minutes. Unfortunately since then it cannot boot.

I remembered that a minute or less before the system froze Firefox message box appeared telling me that some script became irresponsive. I don't remember my choice (kill it/wait).

Hardware: Gigabyte GB-BACE-3160 Brix PC with Hitachi HTS725032A9A364 2.5" HDD and 4GB LPDDR3 RAM (default clock).

More details [here]