It appears to me that the code simply requires a minimum of two 20-amp circuits to serve the kitchen / pantry / dining areas. It does not require both circuits to serve the countertop, or restrict their use to countertop appliances.
Concievably, you could run the circuit without GFCI protection to all receptacles, except those serving the countertops.
I believe that the commonly held belief that the two circuits can only serve the countertop is based upon a pair of misconceptions.
First, the 'no other outlets' can be read to mean 'no outlets in other areas,' and maybe even 'you can't have the lights on them.' I don't see it as meaning 'they can only serve the countertops.'
Second, I think we are confusing good design with code compliance. After all, it has been routine for us to put the diswasher/disposal on its' own circuit, as well as the fridge, and sometimes even the microwave. These were/are design choices, not code requirements.
