As you've found, the dataset_metadata.xml file only affects user-defined properties of the dataset, not the standard columns like visit date and participant id. We should make this as an option. In the mean time, using query metadata seems like a fine way to go. You won't have the ability to import/export this metadata, but I believe you're doing this all in a module anyway.

As for the lookup discrepancy you found, that sounds like a bug. I'll open an issue to investigate this during 10.3.

Adam