(B) Small Appliances. (1) Receptacle Outlets Served. In the kitchen, pantry, breakfast room, dining room, or similar area of a dwelling unit, the two or more 20-ampere small-appliance branch circuits required by 210.11(C)(1) shall serve all wall and floor receptacle outlets covered by 210.52(B) ...
They all have to be in a small appliance circuit and that can be more than two. In a practical sense that only means you feed the dining room and breakfast nook with a 20a circuit instead of a 15a and that only serves receptacles in those 210.52(B) rooms. As long as you have the two 20s on the counter tops and the dining room is on another 20, I doubt most inspectors would bust you for picking up a living room side receptacle on the other side of the peninsula but it is a violation. You can't just go daisy chaining around the room tho.
If you are doing code minimum yes, that dining room receptacle will be AFCI and you will pick up your counter top on a GFCI behind the AFCI. Cutler Hammer has a combo GCI/AFCI that might be handy here. The question probably comes with a "great room" design where there is no real definition of where the kitchen, dining room and great room start.
There's no reason, from a code standpoint, not to just have a separate, 20-amp, AFCI-protected circuit serve the dining room.
Sure, you might set a crock pot on a table ... that's the reason dining rooms are considered as part of the kitchen area ... but I don't see that table as meeting the 'countertop' that would require GFCI protection as well.
There's certainly no requirement that this circuit have anything to do with the kitchen or the kitchen counter. Code simply says you'll have at least two circuits serving the entire area - and that these circuits cannot serve other areas as well.
In this case, the AFCI requirement is certainly a 'curve ball' tossed our way!