First of all you need to get want YOU want regardless. Remember he works for you, you are paying him. You make the decisions. He should have asked.

As for the height. My perimeter counters are the stardard 36" high. My island is 37.5". I posted here as I was concerned about the difference. Apparently many purposely raise or lower parts of their counters. The height of those using the kitchen is important to consider.

For me I ended up liking the difference, but wouldn't want the whole kitchen that height. I'm 5'5".

What about the flooring?

If you counters are too high your range and dishwasher may not fit correctly. You better check the appliance specs. They usually give the necessary space requirements

My finished counters will be even taller than yours but I am 6'1'. My contractor and I went through a lot of discussion about how to make the higher counters happen, because that is what I want.

My opinion? Don't fiddle with the stone. Plain and simple the cab guy needs to fix his mistake of shimming them up. Is the hardwood floor going to be the finished floor level? Tell him that, and tell him you never said anything about tiling so he needs to reinstall the cabinets at standard height for your finished floor height.