Empirical evidence (a failed cron job) shows that cleanup requires the
passphrase (so it presumably needs to decrypt metadata), and though
remove-older-than has been working fine without it, it won't do any harm
to set it in case that changes or there are any special cases.
The problem was that custom records defined for a subdomain where implicit
records are otherwise defined (e.g. A/AAAA records for the root) were ignored.
Though additional_records for a subdomain are processed in the base call to
build_zone (the call for the parent domain), and so custom records that don't
override implicits were working fine, those that overrode implicits were
ignored.
This was because the recursive call to build_zone for the subdomain creates the
implicit records (including A/AAAA records for the root), and so by relying on
the base call to add the additional_records fails because has_rec returned
true.
Adding a subdomain's additional_records in the child call works because has_rec
returns false when testing whether to add an e.g. A/AAAA override for the root,
as the defaults have not yet been added.