You've hit on one problem inherent in trying to make the NEC into a design manual, specifying everything down to the wire-nut level. The problem with such a specific approach to rules is that there are far too many variations possible for 'the book' to address them all.
Heck, we can have trouble defining 'rooms,' let alone specific ones, such as bedrooms, kitchens, and baths. Sometimes it almost seems like architects deliberately try to frustrate the rule book!
That said .... at some point 'common sense' and 'professional judgement' have to come into play. While some might say 'just add GFCI devices to an AFCI circuit,' that really doesn't address the design issues; you almost certainly want to follow 'kitchen rules' regarding counter receptacles and dedicated circuit(s). If you want to fish a multi-wire circuit to do this, you can rule out any sort of AFCI protection. With the similarity in hazards to a kitchen, I think you really want GFCI protection.
So, I reccomend you go back to the very beginning; discuss, in detail, your customers' specific plans, for that specific job - and make your best design code. It's a pretty poor inspector that would let the 'letter of the law' get in the way of good design.
