OK, so where in that article did it actually confirm that Rare is thinking about moving back to Nintendo? It's about making 3DS games for Nintendo, not fully going back to them. This isn't the first time Rare has made handheld games for Nintendo, even when they were part of Microsoft.
DK64 is more likely to come on 3DS if we have Rare working with Nintendo. It's a popular Rare game, so they would probably think about it.