im looking for advice on the patching of these peculiar rust spots.

 

I know that rubber/metal trim between the windshield and the metal is tricky to remove. You can easily bend those pieces.

You may want to try and find out why water remained there and caused rust. Not sure how water drains up there.

Please put the year, model, accord in your signature, so we don't have to ask.

 

SWAG but that kind of looks like a 5th gen (94-97) EX.

Clean the moonroof drains.....four, one from each corner of the moonroof.

Patching, well that is going to depend on how far those iron jawed termites have gone? Also how far you are going/wanting/can go in the repair.

You might be able to hit the spots with a 3m disk/pad that will remove the paint and most of the rust......hope it is not all the way thru the roof skin but I'm guessing it is. Then a good brand of rust converter/preventer. The rest is going to depend on how far you had to go....

My point, it is hard for anyone to really know what is really going to be needed until you start going in.....then once you are there you will know what is really needed.

 

My initial thoughts were to grind it out at the top... and yes it is all the way through which is causing it to leak when it rains. Have you heard of all metal? it is a filler like bondo which will prevent this from happening again?