I decided to cut out the rotten wood and replace it. It's a better overall fix, and it's not really any more work than trying to work bondo.
For the sake of the discussion though, when I was exploring ways to form for the bondo, I used some scrap 1/8 plywood and wiped a smear of petroleum jelly across it. I let it sit long enough for it to absorb into the wood and then I wiped the excess. I applied some bondo across the board. After it cured, the part that was over the Vaseline part peeled off smoothly. The rest of it bonded tightly to the plywood.