Yeah thats a lot more rust than i thought, but it looks like surface rust so it's easy to repair. Tho there's going to be a lot more underneath, which isnt visible right now. My advice to you is, given that it's an old car (mk5's are old lol), strip the windshield, take it to a shop to have them repair the rust entirely and have them paint the top then get a new windshield. Sunburns, scratched windshields are mad annoying to drive with in rain or at night. Replacing my old windshield was one of the best mods I have done to my car, no joke.
The layer underneath your paint is likely the base coat/primer. Given that you basically have a chunk of both paint and clearcoat missing, spotless repair will be quite hard. You'd have to sand down the entire roof all the way from the front to the rear, patch the rusted area, sand down all imperfections to get a flat surface and then re paint and clearcoat the whole thing. Or repair the rust, patch the missing paint spot, sand it all down and wrap the roof. That's going to be cheaper but for that complete oem look you'll wanna take it to a profi paint/body shop and have them do it.
Speaking from experience from being around many different mechanics and painters, seeing them how they work on other cars and what kinda stunts they pull, dont cheap out on bodywork and paint. There's a night and day difference between a back alley jack of all trades guy and someone who specializes in bodywork and paint.
EDIT: just went through and re read the original post and my reply. Yeah I was expecting you to have some rust in the groove where the windscreen sits, not outside of it. And that windscreen looks battered and worn out af, so best bet? get rid of it, get the bodywork and paint done then install a new one.
This'll be offtopic but if you want to keep the car and really enjoy it, get some stage 1/stage 2 tune. No mods are needed. no intake, exhaust or anything. It wont sounds as good but the power will be there. These k03 cars are crazy downlow and for city driving. When i was k03 with a stage 1, the power surge at 2.2k rpm was insane. It felt as if i got hit by a truck from behind. Crazy good city acceleration and response time especially when you have to punch it in traffic to take a gap.