Suprised? No. Disappointed? A little.
Started the process of installing my new sunroof today, needless to say, the corrosion under the rear retainer bar need addressing. What are my most practical options (perhaps even temporary ones, pending more major work)?

That's not too bad - far from an emergency. I would sand the rust to bare metal, feather the sanding into the existing paint work, and touch up the spots with primer, paint, and clear coat. Mask-off good paint work on the roof itself and you'll be able to work on that whole flat strip area. That will hold you for a long time to come.