I just noticed while closing the moonroof on my '03 GT sedan with 100k on the clock that the front corners of the underside of the moonroof it self are rusting.  Is this a common issue.  anything I should watch for now??

Common if the car ever spent any time in the rust belt or near enough to the ocean to get the salt spray from the beach.

 

Likely what you see is just surface rust and could be sanded down and painted.

I picked up an 03 Subaru Legacy Outback.  The hood and front half of the roof was showing paint failure.

 

A fellow I work with does auto body on the side and is painting it for me.  As he sanded it down he said they painted right over rust.

 

Poor prep would cause this failure.  I also noticed rust bubbled on the inside of the roof as I had pulled the headliner to get to the roof rack.

i've got a complete sunroof track assembly for an 03 single pane style, if you want a non-rusty one to swap out.