Sheetmetal under fiberglass cloth and resin can rust if there was any moisture trapped under or in the cloth when you put it on. To answer your topic question if bondo over fiberglass cloth and resin work better the answer is no, the cloth and resin can seperate from the sheetmetal and cause all kinds of nasty things. If you mean fiberglass filler and not cloth, yes, fiberglass filler works great and better than plastic filler, but fiberglass it coverd with plastic filler because fiberglass is porus and hard to smooth, so a light coating of plastic filler is added to smooth the fiberglass.
At work we use three different things. We will tin knock it the best we can or grind down the weld and the area to e filled. Then we apply a fiberglass putty and grind it down then hit it with 80 grit. After that with use a body filler to fill in the major scratches and figure out any more high and low spots. If neccessary we have a rally fine putty that is used t just fill in scratches from the 36 and 80.