Seems like 2 bugs.
mkconf doesn't save the "AUTO" value from the existing mdadm.conf as
defaults:
# save existing values as defaults
if [ -r "$CONFIG" ]; then
DEVICE="$(sed -ne 's/^DEVICE //p' $CONFIG)"
HOMEHOST="$(sed -ne 's/^HOMEHOST //p' $CONFIG)"
PROGRAM="$(sed -ne 's/^PROGRAM //p' $CONFIG)"
fi
and then the initramfs-tools/hooks/mdadm looks for ^ARRAY and if not
found, it doesn't use the mdadm.conf but rather uses mkconf to generate
which of course ignores the AUTO option.
if [ ! -f $CONFIG ]; then
<SNIP>
else
cp -p $CONFIG ${DESTDIR}/etc/mdadm
sed -i '/^CREATE/s/^/#/' $DESTMDADMCONF
if ! grep -q '^ARRAY' $CONFIG; then
tmpfile="${DESTMDADMCONF}.tmp"
if /usr/share/mdadm/mkconf > $tmpfile; then
cp -p $tmpfile $DESTMDADMCONF
rm -f $tmpfile
