UPDATE: The dealer discovered that the water stains on my headliner were from a leaky sunroof gasket. The leak was worst at the right rear corner. The sunroof drip tray's 4 drain hoses were all properly connected and were not blocked by debris. Apparently, the volume of rainwater getting past the gasket was so great it overwhelmed or simply sprayed past the sunroof's drip tray and ended up on top of the headliner, where it ran back toward the rear window and the C pillars. From there, it dripped down into the rear seat belts/retractors, staining the seatbelts. There may also have been a small rain leak from the SIRIUS roof antenna.
Even after the parts arrived, the repairs took several days to complete. The dealer replaced the sunroof glass with its integral gasket, the headliner, the roof antenna, and the rear seat belts. They tie-wrapped the drain hose connections as a precaution and adjusted the closed position of the new sunroof glass to be a little higher in the roof opening so water won't pool on it so readily. The new glass seems to have a slightly thicker or puffier gasket than the original one, so that should help too. All parts and labor were covered under warranty.
The dealer's technician did a careful and thorough job and is confident that the problem has been corrected. He told me that my Legacy is the second new one he's seen with a leak like this. We haven't had any heavy rain since, so I'll have to wait and see if all is well.