Yes it is possible. You can turn a board and transition to the original staining the new floor to match and then match the sheen level of the new to the original. You are best served using a knowledgeable pro for this job. The most satisfying result would be to finger in the new to the old then sand it all. Properly done it will all appear to be original.

So after re reading your recommendations. It sounds like even if I moved to duraseal stain instead of Minwax, I could still have an issue with not just the Bona hd but any Bona poly waterbase or really any waterbase poly?? Do u recommend if I really want the waterbase then I Shd stick with either water pop and then one stain coat and I can use any Bona waterbase unless I use Minwax stain then I need to make sure to use Bona one or Bona mega or Bona domo? Do u prefer the pallmann pall-x to Bona? Also is it okay to do a dye then stain and then waterbase poly? Sounds like another option is to find an oil poly like duraseal matte that perhaps won’t make the ebony like amber once the oil is applied? When u use the oil do u also do three coats? Do u wait 72 hours between oil base Poly applications? Do u think a poly oil would be as durable as Bona hd or Bona one or mega? I don’t really know what this Bona domo does. My floor guy picked it up to try. And the Nordic seal which a bigger problem. I also have a duraseal waterbase poly to try. We feel like it’s a perfect storm and so hard to finger point the issue. Is it the Minwax, is it the drying time not being long enough, is it not sanding to 100, is it the Brazilian cherry? I Shd have just pulled it up but I have so much of it. The oak upstairs looks fabulous. Sorry for the long windedness you have just been so helpful. 🙏🏻

The new upstairs addition is a just big dormer in the shape of a rectangle that doesn’t span the entire length of the house and comes off the back. The entire upstairs has the sloped roof walls but in the area of the addition the ceiling is at normal height. The area was an attic crawl space and never had flooring. About 2/3 of the dormer is going to be a bathroom so it will be a different room and there will be a one inch step up through the door. But 1/3 of the new area that has no flooring (about 40 sq feet) will not be partitioned off from the rest of the bedroom with a door. The contractor thought about using that area as a closet but there is a window on the dormer at that location and we didn’t want to lose the natural light. So the little space will have three walls but be open to the room. We were thinking about making it into a little seating area with two chairs and a table for reading. I thought it might look ok to have carpet there if we can’t match the old pine wood.

The marks are all from bad craftsmanship. You have quite a bit, so a redo is the best way to fix the issue. Confirm that your flooring is at it's limit for sanding by sticking a business card in a gap and mark the depth. Then remove and measure the width of the mark. That will confirm how much wear layer you have. By the looks of it you still have plenty. I do not see any exposed fastneres in the joints. Minimum wear layer is 3/32 (0.93).