"Bondo" is a trade name for putty resin. I don't have any experience with these filler putties, but I've been working in the composites field for darn near forever...at least it feels like it sometimes. There are basically three different components that make up the compound: resin, catalyst, and filler. From the performance perspective, epoxy resins are better than polyesters. ("Bondo", as I recall, is polyester.) Polyester is also the base resin in what is generically called "fiberglass", like the old Corvette bodies.
You add a resin-specific catalyst to get it to change from a liquid to a solid. Different resins require different catalysts. Some catalysts are "hotter" than others. Think of Devcon epoxy that you buy in the hardware store. You can buy 1 minute, 3 minute, and 15 minute epoxies, but this is really just a tweak to the catalyst. Not enough catalyst and your resin will take forever to cure. Too much can make it unworkable. More isn't better.
Filler is the stuff that makes it great for body filling. It is usually pulverized on a microscopic scale- the finer it is, the smoother it can sand out. Too much filler will reduce the amount of resin, sorta like aggregate, sand, and portland in concrete. You want the right ratios.
Like Bill said, you want to make sure you get the right one for the job. Don't think they are all the same because (I believe) each one is formulated for a specific application. You don't want to do the work twice, so I would recommend buying on the expensive side "just in case."
Bill