What you are saying makes sense and anyone skilled should have known what the cabinets are and what the pieces were - we cheated and got a cabinet guy who did my mom's kitchen to help us hang the cabinets and he saw the few minor issues right away and we got them fixed - he fit us in by the day so it wasn't a big deal - had to rework the molding (order fillers) and one cabinet was not plywood sides and it was exposed so he said to fuss and get that replaced. And, our fridge panels were not ordered right, but he figured out how to make them work in our space so you wouldn't know looking at it but one should be another style.
There probably is a way to put a small support in for the countertop but of course the best way is to use the piece ordered by your KD. Oh well. I'd go to HD or Lowes and look at the metal bars if you are that worried and see if you can find some to glue onto the inside of the panel once it is 100% in place to help support the panel and countertop, but my guess is that it will be ok, but I am not a countertop expert. If you get it think enough, your dishwasher is thiner in the inside so you should have some room. But, check with someone who knows more before taking my suggestion.
For the floor, I'd insist at their cost they put trim molding - Kraftmaid makes several types.
Here is ours with the panel - my husband did trim around the panel so you can see it and they can't say it can't be done and he's DIY and never did it before:
Q