I have not done the exact repair that you seek, but do have one plan that I would try if faced with the need to do so. I would use the blue masking tape and tape off the surrounding boards, leaving exposed only the board(s) with the scratch. Hand sand that board with the grain with 180 -220 grit abrasive just to minimize the scratch. Sand evenly over the surface of the board, not just at the scratch. Sanding just at one spot creates a "dimple". Then clean and dust that board. Apply new finish to the entire board(s).

Can't help you much here. For the lightest natural look you should be specifying a commercial quality waterborne polyurethane. For the traditional yellow or amber tones, then oil base polyurethane will give you that automatically when it is applied to the wood. By "clear stain" you must mean a sanding sealer, yes? Any contractor ought to be able to provide samples for you to look at or to do one directly on your floor to show you the results he or she can achieve with the materials he or she works with. There is no set standard for floor finishing...you need to know what the contractor can do. Perhaps somone who works with the oil base products will come in with some descriptions. Good luck.

The amount of vinegar and water you would use with a spray bottle on a dust mop won't "break down the finish". As someone who has spent considerable time removing finishes, it might be easy if it did. Granted, soaking some shellac in vinegar might dull it a bit....but spritzing a dust mop with a bit of the solution to keep the dust down and combat any streaks plain water might leave is a good thing! The thing I object to with Bona is that people wash with it, saturate the finish....and that is never good for wood! You don't slosh a bucket of vinegar water on your floors, put a little spritzed on your dust mop will be lots better than Bona, Orange goo, Murphey's stuff or anything else you can imagine....but for perhaps mineral spirits....and nota's not a good option for weekly cleaning https://howtohardwoodfloors.com/vinegar-clean-hardwood-floors.html

Oil based finishes impart that amber tint. When water based finishes first appeared, the lack of that amber tint created enough of a different look people were bothered by the plainness. Now, stains and tastes have changed enough for folks to accept the lack of tone. In your case, you want the water based type. Using a water based finish over the oil stain should be no problem. Just follow the instructions from the manufacturer of the finish you select. I've used MinWax poly for floors(different than regular poly?), but I used the oil based variety because I wanted that amber tint. There are several types of Bona floor products.