We are using several ISV and also adding custom fields to the AX database. We have found that the fields are visible in the target table and we can add the fields to the staging DMF* table that corresponds to target table.
It appears that there is and XML table, DMFTargetXML table that needs to be updated before you and set the DMFTargetXMLToEntityMap(DMFTargetXMLToEntityMap). The DMFTableXML cannot be edited in the AOT and I cannot find a job, class or method that updates this table with the newly created fields.