Why would they bother to make Madden 2001 blue or Rayman 2 green and not charge the end consumer more if there was any significant associated cost? I could see there being some difference, but I find it hard to believe it'd be anything more than a 2-3% increase per cart(around 50 cents). The idea that there would be any substantial increased cost reeks of bullshit, or else why would any third party ever do it?
Besides, the original discussion was about Donkey Kong, a Nintendo IP, so whatever is in any leaked development partner catalog is a moot point. Injecting existing plastic molds with a different color plastic would be trivially cheap, even in the N64/GBC days.
Back in the day, each cart was a custom board that had to be custom designed and manufactured. I'd say the reason colored cards aren't generally done for systems like DS, 3DS and Switch is because the cards are standardized and don't have custom PCBs, therefore they are just mass produced as blank cards and written later, whereas with the old PCBs you had to have a custom run for each game. Carts were basically plug in ram that interfaced directly with the system's cpu as memory whereas the cards Nintendo has made post GBA are more along the lines of a custom type of flash memory similar to an SD card that is written after the fact.