Comment 5 for bug 1287436

1)
Warning: Setting GRUB_TIMEOUT to a non-zero value when GRUB_HIDDEN_TIMEOUT is set is no longer supported.

This warning is because of https://bugs.launchpad.net/ubuntu/+source/grub2/+bug/1258597
I was able to solve it by:

function Fix_grub_config() {
  if grep -q "^GRUB_HIDDEN_TIMEOUT=0$" /etc/default/grub || grep -q "^GRUB_HIDDEN_TIMEOUT_QUIET=true$" /etc/default/grub; then
    echo -en "ACTION:\tFixing Grub config... "
    sed -i "s/^GRUB_HIDDEN_TIMEOUT=0$/#GRUB_HIDDEN_TIMEOUT=0/" /etc/default/grub
   sed -i "s/^GRUB_HIDDEN_TIMEOUT_QUIET=true$/#GRUB_HIDDEN_TIMEOUT_QUIET=true/" /etc/default/grub
    echo "Done."
  fi
}

But this fix brings up a new issue for me personally. When running the dist-upgrade, it now shows a pop-up from "grub-pc config", complaining that I modified /etc/default/grub asking me what to do.
As I'm trying to run the dist-upgrade non-interactively, this is a bigger issue for me than the warning, so I will not perform this fix...

2)
rmdir: failed to remove `/var/lib/os-prober/mount': Device or resource busy

By using set -xv I was able to track down this issue a bit further:

/usr/sbin/grub-mkconfig -o /boot/grub/grub.cfg
--> /etc/grub.d/30_os-prober
--> OSPROBED="`os-prober | tr ' ' '^' | paste -s -d ' '`"
--> /usr/bin/os-prober
--> /usr/lib/os-probes/50mounted-tests /dev/sda5

if [ "$mounted" ]; then
                for test in /usr/lib/os-probes/mounted/*; do
                                debug "running subtest $test"
                                if [ -f "$test" ] && [ -x "$test" ]; then
                                                if "$test" "$partition" "$tmpmnt" "$type"; then
                                                                debug "os found by subtest $test"
                                                                if ! umount "$tmpmnt"; then
                                                                                warn "failed to umount $tmpmnt"
                                                                fi
                                                                case "$type" in
                                                                    btrfs)
                                                                                # umount to account for the bind-mount
                                                                                if [ -x "$tmpmnt/@/lib" ] && \
                                                                                   ! umount $tmpmnt; then
                                                                                                warn "failed to umount $tmpmnt"
                                                                                fi
                                                                                ;;
                                                                esac
                                                                rmdir "$tmpmnt" || true
                                                                exit 0
                                                fi
                                fi
                done
                if ! umount "$tmpmnt"; then
                                warn "failed to umount $tmpmnt"
                fi
fi
+ [ ]

rmdir "$tmpmnt" || true
+ rmdir /var/lib/os-prober/mount
rmdir: failed to remove `/var/lib/os-prober/mount': Device or resource busy

PERSONAL CONCLUSION (please correct me if I'm wrong):
Although it is not nice, I don't see anything dangerous in not being able to successfully unmount a FS and clean up that folder.
After a reboot (which I do anyway), most of this should be solved anyway...

3)
grub-probe: error: unknown filesystem.

By using set -xv I was able to track down this issue a bit further:

/usr/sbin/grub-mkconfig -o /boot/grub/grub.cfg
--> /etc/grub.d/30_os-prober
--> OSPROBED="`os-prober | tr ' ' '^' | paste -s -d ' '`"
--> /usr/bin/os-prober
--> /usr/lib/os-probes/50mounted-tests /dev/mapper/vgos-rootsnapvol
--> grub-probe -d /dev/mapper/vgos-rootsnapvol -t fs

I'm able to reproduce the error and by changing the path a bit also to solve it:

root@dcmilphlum173:~# grub-probe -d /dev/mapper/vgos-rootsnapvol
grub-probe: error: unknown filesystem.
root@dcmilphlum173:~# grub-probe -d /dev/vgos/rootsnapvol
ext2
root@dcmilphlum173:~#

although both paths seem the same:

root@dcmilphlum173:~# ls -la /dev/mapper/vgos-rootsnapvol
lrwxrwxrwx 1 root root 7 Mar 18 06:30 /dev/mapper/vgos-rootsnapvol -> ../dm-6
root@dcmilphlum173:~# ls -la /dev/vgos/rootsnapvol
lrwxrwxrwx 1 root root 7 Mar 18 06:30 /dev/vgos/rootsnapvol -> ../dm-6
root@dcmilphlum173:~#

PERSONAL CONCLUSION (please correct me if I'm wrong):
Also here I don't see any big danger, as grub shouldn't do anything with those snapshot volumes anyway...