we refinished old oil stained floors with amber seal & it did a good job evening the tones in a couple spots where the old oils penetrated really deep into the grain. I had been worried that it is called amber but found it has more of a warm vanilla look very clean light & natural.

We had our 2 1/2" top-nailed red oak floors refinished with some kind of water-based Bona Natural seal...no stain...almost 2 years ago. The nails are visible in the existing floor, which were sanded enough to remove the stain; nails are not as visible on the matching floor we had them install in the rooms that had previously been carpet. I thought the nail visibility had more to do with how much floor was sanded down to remove the pre-existing stain. Nothing is rusty.

You have choices. 1) You can do the floor natural color and use all water based products to eliminate residual odors. 2) You can use a reliable oil based stain that is formulated to use with water based finishes and perhaps have some residual odor. 3) You can use water based stain and when the application is predictably unacceptable, you can choose selections 1 or 2 above. Other than water based aniline dye applied at full strength, I've not seen an acceptable water based wood floor stain. Which one were you looking at to recommend to your contractor?

You want to avoid applying a second coat of stain. It will cause adhesion issues. What you can do is add some of the stain to a oil base poly, then apply it. Another option is to use poly shade in a similar color. You can apply 2-3 coats of the poly shade to achieve your desired color. Poly shade is oil base. Contractor should have water popped the floor prior to applying the stain. The color would come out darker.