During the import process in ePO you can select to map a V5 User Group to an LDAP Group.
This is actioned by going to Menu -> Encryption Users -> Tasks -> Import v5 user assignments -> When you reach step 4 select the v5 user group -> Action -> Assign an LDAP group.
I think you misunderstood. I have been doing that and it works fine.
But how do you map the LDAP user/ security group or computer to an ePO OU (let's go with AD talk). I don't have a flat ePO OU Structure.