Er, that's not entirely true. In fact, there were several Rare-published games on the N64 including Jet Force Gemini, Perfect Dark 64 and (I think) Diddy Kong Racing.

Nintendo-published titles would include Goldeneye, Banjo-Kazooie, Blast Corps.

There was a definite difference with the publishing arrangement for these games because it took longer for your bonus to come through if you worked on them!