You are right that when booking award seats on LH using UA miles, United (as the booking agent) creates a record locator and issues a 016 ticket, while Lufthansa (as the reservation holder) creates a separate locator. When referencing any travel by phone or online with LH, the United code will mean nothing to them.

Actually I tried exactly the above method (calling UA) just today without success. Despite being 1P/Gold, my call was routed to India and the agent, though friendly, was not able to provide me with Lufthansa's unique pnr#. Note that this information was formerly accessible (and quite conveniently) in the pre-merger version of United.com.

My workaround was to call Lufthansa -and provide them with my name, date, and flight numbers. They were then able to provide me with their unique record locator, and assign seats over the phone. I can now also check the details and refine seats on Lufthansa.com using their code.