I spoke to Apple CS on chat and she told me you could - as long as it's the same price and the band you want has the same Watch/band combo you will end up with. I.e. Can switch from sport to nylon on the aluminum series 2 models... the rep did say this had to take place in the original 14 days.
They'll do this in store or online?
Because the way you are describing it is the only way it worked last year. As in:
Person buys a 42MM SS with WSB, but really wanted the 42MM SS with BSB.
Or
Person buys a 42MM SS with Milanese, but really wants a 42MM SS with Midnight Blue LL.
In both cases, cost of entire watch (or cost of band, however you look at it) is the same and the combo is one that is offered in an intact watch.
So, if you bought a 42MM Silver Sport with a WSB and you wanted the Pearl Nylon, you could switch, but if you wanted some other nylon band, they wouldn't allow it.
Or, that's how it worked last year. And, it was all done online.