To start off, Bondo is a brand and the generic term for filler. There is a difference amoung them. The main difference is the staning. Most of your high end fillers are stain free. That means that they will not stain. Cheap fillers have the chance of staning. That is where you see stains in the paint from the filler, no primer or sealer can stop it. If something stains from the filler you must remove the filler and start over. Its mostly seen in white and other lite colors. Like I said it does not happen all the time but there is a chance. Now the higher end fillers are stain free and yes they are higher in price. Most go from 18 to 25 a gallon, and they do say stain free. Todays fillers are very durable if used right. The fillers with metal chips in them are very good fillers but they are much harder to sand and price is around 70 a gallon. As for the primer-filler-primer thing in some cases that is good but most heavy fillers must go to bare steel, the directions on the can will tell you. You can still primer your car but places you need to put filler just grind the primer back off. If its just light dents that you are working with some lightweight fillers will go to primer you can just scuff the spot that needs to be fixed and just apply the filler to the spot. In the end all filler needs to be primed you really should not seal or paint over bare filler. As for primer stopping rust, if you take a part and strip it down to bare metal and let it set out in the rain and elements it will still rust, you may not see it but primer is porus. Now if you take a part down to bare metal and primer it and it stays in you garage and does not get wet all the time you are good. If you are doing an restoration and have something sand or media blasted when you get if back you need to get it in primer as soon as possable the primer will help surface rust. And that is where the primer filler primer thing comes in. If your vehicle is in primer it somewhat helps to see the dents, so depending on what type of filler you are useing you can grind the primer off and apply the filler and then reprimer or you can just scuff and use a filler then reprimer.