My Imusa mug with fuel, lighter, heat reflector, wind screen, and spoon go in the top of my pack on one side. Food gets packed around and next to it. Jacket goes on top, since if I'm stopping to cook, I'll want to put something on to stay warm. It might provide some extra padding as well. I've definitely flexed the aluminum pot, but not bent it. Yet (knock on wood).
I've started keeping my cat can stove on my person in order to keep it warm. I've discovered that a cold stove takes forever to blossom, whereas one at body temp goes right up, regardless of the temperature of the alcohol. I waste a lot less fuel waiting that way.