@grumpygamer in most games, double damage is a temporary thing, I think. And then when activated it would double whatever you had at that moment. So even as a permanent bonus I would go with applying it last.
Also if the game were heavily using/relying on +x modifiers then it would feel like a rip-off to me if it were only doubling the base damage and by that maybe only adding +10% in reality. Unless it were clearly saying to only double the base damage.