If you are making a hard master, there is no reason you can't mix materials. You can make details out of clay, like fins, bake them hard, and glue them to your wood master, for example.
As long as it holds together when you pour in your silicone, you're good to go.
You can also use bondo to fix errors, like Dave said, or to add material to areas where you want to carve details.
Bondo carves really easily. I even used it to add a lip bump to the aluminum prop fin on one of my whopper ploppers, and it let me give some shape to the lip's otherwise flat surface. I did sand the lip first, for a mechanical anchor point, and then coated the finished bondo with super glue, to reinforce it, before I painted it and dipped it in Solarez.