The following will reproduce the issue in a disco VM with disco LXD container:

Initial setup:
1. have an up to date disco vm
$ cat /proc/version_signature 
Ubuntu 5.0.0-11.12-generic 5.0.6

2. sudo snap install lxd
3. sudo adduser `id -un` lxd
4. newgrp lxd
5. sudo lxd init # use defaults
6. . /etc/profile.d/apps-bin-path.sh

After this note the SFS_MOUNTPOINT bug:
1. lxc launch ubuntu-daily:d d-testapparmor
2. lxc exec d-testapparmor /lib/apparmor/apparmor.systemd reload
3. fix /lib/apparmor/rc.apparmor.functions to define SFS_MOUNTPOINT="${SECURITYFS}/${MODULE}" at the top of is_container_with_internal_policy(). Ie lxc exec d-testapparmor vi /lib/apparmor/rc.apparmor.functions 
4. lxc exec d-testapparmor -- sh -x /lib/apparmor/apparmor.systemd reload # notice apparmor_parser was called

At this point, these were called (as seen from the sh -x output, above):

/sbin/apparmor_parser --write-cache --replace -- /etc/apparmor.d
/sbin/apparmor_parser --write-cache --replace -- /var/lib/snapd/apparmor/profiles

but no profiles were loaded:
$ lxc exec d-testapparmor aa-status

Note weird parser error trying to load an individual profile:
$ lxc exec d-testapparmor -- apparmor_parser -r /etc/apparmor.d/sbin.dhclient 
AppArmor parser error for /etc/apparmor.d/sbin.dhclient in /etc/apparmor.d/tunables/home at line 25: Could not process include directory '/etc/apparmor.d/tunables/home.d' in 'tunables/home.d'

Stopping and starting the container doesn't help:
$ lxc stop d-testapparmor
$ lxc start d-testapparmor
$ lxc exec d-testapparmor aa-status
apparmor module is loaded.
0 profiles are loaded.
0 profiles are in enforce mode.
0 profiles are in complain mode.
0 processes have profiles defined.
0 processes are in enforce mode.
0 processes are in complain mode.
0 processes are unconfined but have a profile defined.


Note, under 5.0.0-8.9 and with the SFS_MOUNTPOINT fix, the tunables error goes away:
$ lxc exec d-testapparmor -- apparmor_parser -r /etc/apparmor.d/sbin.dhclient
$

and the profiles load on container start:
$ lxc exec d-testapparmor aa-status
apparmor module is loaded.
27 profiles are loaded.
27 profiles are in enforce mode.
   /sbin/dhclient
   /snap/core/6673/usr/lib/snapd/snap-confine
   /snap/core/6673/usr/lib/snapd/snap-confine//mount-namespace-capture-helper
   /usr/bin/man
   /usr/lib/NetworkManager/nm-dhcp-client.action
   /usr/lib/NetworkManager/nm-dhcp-helper
   /usr/lib/connman/scripts/dhclient-script
   /usr/lib/snapd/snap-confine
   /usr/lib/snapd/snap-confine//mount-namespace-capture-helper
   /usr/sbin/tcpdump
   man_filter
   man_groff
   nvidia_modprobe
   nvidia_modprobe//kmod
   snap-update-ns.core
   snap-update-ns.lxd
   snap.core.hook.configure
   snap.lxd.activate
   snap.lxd.benchmark
   snap.lxd.buginfo
   snap.lxd.check-kernel
   snap.lxd.daemon
   snap.lxd.hook.configure
   snap.lxd.hook.install
   snap.lxd.lxc
   snap.lxd.lxd
   snap.lxd.migrate
0 profiles are in complain mode.
0 processes have profiles defined.
0 processes are in enforce mode.
0 processes are in complain mode.
0 processes are unconfined but have a profile defined.

However, 5.0.0-11.12 has fixes for lxd and apparmor. This 11.12 also starts using shiftfs. Very interestingly, if I create a container under 5.0.0-8.9, do the SFS_MOUNTPOINT fix and start it under 5.0.0-11.12, then policy loads and everything seems fine; there are no shiftfs mounts for that container:

$ lxc exec d-testapparmor -- grep shiftfs /proc/self/mountinfo
$

*but* if I create the container under 11.12, I see the problems and there are shiftfs mounts:
$ lxc exec shiftfs-testapparmor -- grep shiftfs /proc/self/mountinfo
1042 443 0:78 / / rw,relatime - shiftfs /var/snap/lxd/common/lxd/storage-pools/default/containers/shiftfs-testapparmor/rootfs rw,passthrough=3
1067 1043 0:57 /shiftfs-testapparmor /dev/.lxd-mounts rw,relatime master:216 - tmpfs tmpfs rw,size=100k,mode=711
1514 1042 0:78 /snap /snap rw,relatime shared:626 - shiftfs /var/snap/lxd/common/lxd/storage-pools/default/containers/shiftfs-testapparmor/rootfs rw,passthrough=3