If you want some color to the walnut then you would use stain. Although some may use a nuetral stain as a sealer. But generally yes the oil sealer would be the same step as stain. Too many coats? The general standard is a sealer then 2 coats. But having a third coat doesnt effect anything. Some may choose to do the 3rd coat. It all depends on the contractor doing the work. Just make sure that if they charge for that "extra" coat that it is reflected in their bid. When you have someone claiming they will do 5-7 coats is when you should start questioning.

We do this all the time...yes, you can come close to the look of ambered floor finishing film. There are some one step floor sealers coming on the market that will color the wood to give it that yellowish look...they are primarilly professional use products. You must follow stain application rates and dry times. Use a finishing system that is designed for product compatability.

You are mixing chemicals (mastic adhesive + mineral spirits + polyurethane + concrete moisture) and have had a reaction. I've heard this done...but only by high-end epoxy finishers that deal with plastics and chemicals every day; all day. There is a reason why the epoxy finishers are some of the highest paid flooring professionals around...you need a degree in chemistry to understand epoxy. And polyurethane for wood is a vastly different product than polyurethane for concrete. There are so many things that could have gone wrong (didn't rinse the floor after the mineral spirits; wrong polyurethane; moisture coming up from the slab; mastic reacting with the polyurethane; etc) that it is hard to figure out what is happening. Mastic is an aggressive material. It doesn't like anything but vinyl backed stuff. One man's adhesive (mastic) is another man's solvent (polyurethane). Good luck. My guess is you will be using a diamond grinder to get this down to raw concrete so that you can start over.

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.