Rigid sheathing over the patch should do just fine. The height difference in the two floors isn't something you can help. If you feel that it is worth the effort and the price, you can ask him to stop and REMOVE the top layer of subfloor. Then ask him to REPLACE IT with NEW plywood. This will NOT change the roller-coaster waviness of the surface. That is inherent in the house. It will simply give you smooth "new" while keeping the two floor heights as close to even as possible. If the height variation upsets you, then you have two options: choose sheet material like sheet vinyl or sheet linoleum or rip out and rebuild the entire kitchen floor and *possibly the entire main level. My suspicion is the KITCHEN floor was raised to meet/match the other flooring. If that is the case, it is possible to remove the current plywood and then drop in slightly THINNER plywood. Again....this all hangs on the question as to whether or not the kitchen subfloor was raised to meet the other flooring. You are not allowed to go "too thin" with a subfloor. Most industry standards require (depending on where you live and how old the house is) TWO layers of subfloor that equal or exceed 3/4" total thickness. Sigh. It might be possible to drop the kitchen subfloor a snick. But the amount of money and effort it will take could be a deal breaker. It should have/would have been talked about BEFORE he started patching. And I mean WAAAAAAAY before he started patching. Like several WEEKS before he stepped on site. This would have been discussed because you would have CHOSEN your floor and discovered the difference and would have raised the possibility at the time. It's not too late...but then again you don't want to see his face after you tell him to rip out his work and start again...with new plywood, etc.

@Judy Frank are the ”saw” marks these textured stripes that run horizontally throughout the planks? my sample board of Finally Mine has them and wasn’t sure if defect of sample or true of the floor overall. Does anyone have experience and insight on these ”saw marks” sometimes I see them referred to as ”cut marks”

They are holding up just fine. The one thing I would do over again is not have them install the 1/4” round at the walls. My walls already had crown molding on bottom of walls. Buffalo Floors and Up simply decided to go up to existing crown molding and then laid 1/4” round for transition. In hind sight I would have removed the crown molding and had them lay planks to the wall and relay the crown molding. Hind sights 20-20 though.

Do you mean the cabinet or a wood counter .I will say I do not like real wood next to fake but I need to see all your choices .If you must have wood stain then I would probably coose the darkest color from the flooring that will make the whole thing easier. Could you post pics of the cabinets appliances etc to give us some idea of your space.