I have been using reinforced glass bondo on my screen as well. I have found that if you smooth the bondo with you finger as it dries it will be much smoother when dried. After you have sanded it pretty well, then use regular bondo to fill in the holes. But use very light layers of the regular bondo, just enough to fill in the holes. Sand and repeat with bondo again to get a smoother finish. From what I have found, if you don't use light coats of the regular bondo, you will get holes just as before. And you will have to do a lot of sanding if you want to get a really smooth finish.
My screen looked similar to your in the pictures, you just have to sand it more. I did alot of sanding on mine, got it pretty even before I used the regular bondo.