Unfortunately, the baking soda reacted with the wood and has "weathered" it. I don't think there is a way to fix it other than covering all the wood up with paint, a dark stain, or, applying a baking soda mix to everything so it matches. Baking soda reacts with tannins in the wood. Pine doesn't have tannins that I'm aware of. I cannot tell if the wood is indeed pine, or cedar, or something else. Looks like the wood just has a linseed oil finish. But linseed oil would not bring that much color out of pine. If it is pine, most difficult thing would be matching the color. You may be able to sand it out.

Hi Lola! Depends in part on what specie/color of wood you used..... That looks like pine so you could probably use a clear oil like Messmer's UV+ and accomplish the same thing. It will darken the wood a little bit and bring out/maintain the natural colors. If you have any boards left over, to get a very specific color, have the person who will be applying it for you create a couple samples and test it on small swatches until you find the one you're looking for. Best of luck and let it know how it works out! https://www.soluslumber.com/shop/supplies/deck-seals-oils-finish/

I like the look now and wouldn't stain it, the problem with leaving it would be the way it coordinated with the wood floor. That said, I'd either leave it and change the floor color or make the contractor paint it. One question: Did the T&G sit in the house for two weeks with heat/AC running to acclimate it to the temp/humidity? If not, it's going to shrink or swell (probably shrink) when the house is closed up and heated/cooled. If you paint, you want to paint AFTER THAT. Otherwise, you'll have lines of unpainted pine showing through. The house will be near finished and the contractor will say "You really don't notice it from down here" and won't address the issue.

I‘m a little late to the game,but maybe this will help someone else. you can solve this blotchiness with a stain sealer (sanding sealer, de waxed shellac, etc....) cut with mineral spirits up to 50/50 will solve this problem. you can test with a thin coat of 100% sealer, a 75:25 sealer to Mineral Spirits ratio then a 50:50 Ratio to see which works best. A pre-stain conditioner might help, but doesn't always work as well.. Some types of wood - notably pine, maple, birch and cherry, do not like to take stain evenly so by partially sealing your wood first you will get better results.