I don't plant golden seal, mostly because invasive Japanese barberry root does exactly the same thing and is ridiculously abundant. I think you have to consider the growing conditions. If they're the same then they should stratify similarly, especially since they are both under-story plants. If I were you, even if you stratified them in the same barrel I'd separate the ginseng and golden seal with a layer of burlap, or perforated plastic. That would reduce the risk they will mix.