I've just looked up a bunch of Rareware games, that looks like it could be the case. Banjo-Kazooie, Blast Corps, GoldenEye 007, Killer Instinct Gold are published by Nintendo and are in a black frame
Meanwhile, Conker (Published by THQ) & Perfect Dark (published by Rareware)
But if this were true, then something's wrong with Banjo-Tooie:
https://vgcollect.com/item/24708 Banjo-Tooie came out a lot later that these other games right? Maybe Nintendo changed their packaging regulations / branding policies, maybe they just got more lax about the whole process.
Pokémon Stadium & Pokémon Stadium 2 (supposedly published by Nintendo) also do not use the black frame. These Pokémon games also came out 2000 / 2001 respectively.