I know this is a relatively old post, but I thought I would share my
experience. Our machines on 10.13 and 10.14 in APFS format were not
showing that a recovery volume / partition was present. Like you, I ran
a diskutil list and saw that /dev/disk1s3...
I deployed the 'custom setting' and it appears as though it's getting
overwritten by the root level managed preferences. I eventually had to
deploy a restrictions/functionality payload alongside my FileVault2
security & privacy payload. It'll be nice...
