Dyna Glass has glass strands mixed in it. Bondo doesn't. For repairs that are deeper(thicker) using something like Dyna Glass will help ensure that it will be less likely to crack. For things like scratches using a glazing putty like Evercoat is better. It's all about the type of filler used to make the putty. Some are stronger, some are easier to sand. I like to use gel coat and add my own mix of fillers depending on what needs to be done.
That is my preferred method as well, that is mix up some gel coat with colloidal silica West Systems #406(wear a mask when using this stuff, it will shred your lungs)to the point to where it has the viscosity between mayonnaise and peanut butter. My Prindle's and 5.8 have plenty of these
little patches on them and they held up very well.