I think it makes more sense. Think about it. That market has MTs so ridiculous as to getting x raw material items for a penny or so. So what about having the once-a-day system for getting does. Not only the amiibo feels like a premium item but also the functionality fits more to what it does in the Wii U and 3DS. I mean; extra hearts with Zelda, extra arrows with Link, a skin in Mario Kart for your Mii, a small easter egg with Toad in Captain Toad.
I think those small things might be more valued in a mobile game do to the model embracing those kinds of transactions more openly. Given they're smaller games you play daily you might one to use the amiibo more and finally instead of spending a penny for a small transaction the amiibo then becomes a premium item giving you a free amount per day.
Well, at the very least that's my thought process applied to any other company. I don't know what Nintendo would do. They might just put advertisements for their games in them.