Node Reference Fields Require Modification Via prepare_node Hook

I was trying to import a node reference field and I got everything set up correctly via Table Wizard and a relationship using the generated node_map table. In my table analysis, I set up the correct pointer for pulling in the necessary node id into my node reference field, but during the migration, the field wasn't being populated at all. I noticed that the node field doesn't appear to be being named correctly for some reason. The data should actually be going into $node->field_release[0]['nid'], but it's actually going into $node->field_release_nid. I used HOOK_migrate_destination_prepare_node to fill in the correct field:

$node->field_release[0]['nid'] = $node->field_release_nid;

I was thinking that this is something that should work easily out of the box and shouldn't require the use of the hook, but I could be wrong.