In your situation, and I know this isn't really what you're asking, I like to utilize the five foot rule. If you can't see it from five feet away, its not a problem. What I mean is, you are going to have a dining room table in your dining room (assumption I admit, but a safe one I hope) The table is going to induce lighting and shadow variations on your floor which are likely to mimic the color variation you describe, I hope. In addition, you may be considering some kind of area rug in the dining room, ie oriental carpet.
I'm sure a professional floor guy could give you some great answers, but I think you have some mitigating circumstances here.
Remember the phrase: "It's the natural beauty of wood!"
and, "it's a hundred years old, not a factory finish"
Hope that helps, I don't mean to minimize your concerns, and I wish I could see your home, it sounds beautiful!