Yes my friend Comm. The bones you don't use to weight a mesh, are not included when compiling the animation. The best, and more accurate, solution I figured, is to make meshes out of copies of the bones and weight each and every one of them to their respective bone. That's why you can see the bones as meshes in ModView after compiling, cuz they are meshes =).
About the DaVinci sindrome, you only have to set the first frame of your sequence to the DaVinci pose, or your anims will get their ass twisted after compiling.