I'm not sure about the DNS-part, I tried to look for an RFC describing this configuration but wasn't able to find anything, maybe you got some useful info?
I checked with the people at Comodo who authored RFC 6844 for CAA and got this back:
If there are no records in the zone, there are no CAA records so the discovery continues up to .com which will also have no CAA records and so there will be no constraints on issue.
If the zone is DNSSEC signed and the data is unavailable, the CABForum rules would require the CA to refuse to issue.
Ballot 187 – Make CAA Checking Mandatory – CAB Forum states:
CAs are permitted to treat a record lookup failure as permission to issue if:
the failure is outside the CA’s infrastructure;
the lookup has been retried at least once; and
the domain’s zone does not have a DNSSEC validation chain to the ICANN root.
So I'd assume that LE would be able to accept our use case as a lookup failure and go on to the next step in their validation.