As long as all the woods coordinate tonally (so that the juxtaposition doesn't make one or another look very orange or very yellow, say), they can be different colors. For that matter, small differences in color between floors are unlikely to be picked up by the average eye.

So many concerns

FIVE coats of stain? Recipe for polyurethane bonding issues

Only two horizontal bars on new handrails? Sounds like a code violation

To your question, one kind of flooring everywhere makes a house seem larger and more harmonious (excluding bathrooms etc)

Thank you for your insight and for responding so quickly. I'm attaching some photos, as the colors are rather different. Its difficult to see from the picture of the stairs before the carpeting and old railing was removed but the flooring has dark knots in it that the Jacobean stain mimic and compliments nicely (the existing wood floor also appears a bit lighter in this picture than it does in reality) The second picture is a sample of the tread stained in the Jacobean.

Suffice it to say, it would make for a dark contrast upstairs in the hall. Looking down from the upstairs hall it looks fine and "blends", just as you suggested, its looking down from the landing on the turn that I'm concerned won't make for a "cohesive" look

Here's an inspiration pic from which the stair railing is being fabricated in black wrought iron (there will be glass in between so its not a code violation). Can you elaborate as to the potential polyurethane bonding issues? I apologize for my ignorance but would appreciate you putting this in to context for me

First coat of stain sinks into the wood and blocks the pores. The next four coats sit on top. Polyurethane is applied and bonds to the top coat of stain. Floor dries. At some point in the future polyurethane starts to peel off the floor in sheets. Heartache ensues.

I am not anti dark floors as my floors are almost black (every scratch and fleck of dust shows) but you need to buy a stain that is the correct color with one application so the poly can bond to something.

In general I believe that wood floors should coordinate though out a house, but the stairs are an exception to that rule as a special feature. In historic houses for instance when the floors were typically oak, the stair treads would often match the wall trim in wood species and color rather than the rest of the floors. I think the same can be applied to new designs.

I think your two woods can go together as the dark stain picks up the dark tones in your wood floor. But I would caution as mentioned above especially on a stair where there are many edges that can be caught that you may find that scratches are pretty prominent and will need to be touched up.

I SOOO appreciate all the advice, although now I have a whole new set of reservations. I've attached a picture of the kitchen, as the house is what I would consider transitional. There are definitely traditional elements but also what I guess I would consider modern farmhouse as the wall to the right in the kitchen picture, for instance, is ship lap.

I really like your style. But I’m not sure about choice of Jacobean as I think the pros are right, you need consistency in your flooring. Make your stair railing the show stopper, it sounds lovely.

You don't need five coats of jacobean to achieve the look you want. You need the right process. Your finisher does not know about water popping. I would look for a new finisher.